Starting phenix.real_space_refine
on Thu Sep 18 05:13:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sna_40618/09_2025/8sna_40618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sna_40618/09_2025/8sna_40618.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sna_40618/09_2025/8sna_40618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sna_40618/09_2025/8sna_40618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sna_40618/09_2025/8sna_40618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sna_40618/09_2025/8sna_40618.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      33      5.16       5
     C    8264      2.51       5
     N    2710      2.21       5
     O    3288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14591
  Number of models: 1
  Model: ""
    Number of chains: 14
    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: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    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: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    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: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 3
    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: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    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  12296  SG  CYS K  31      52.091  72.096  45.471  1.00130.70           S
  ATOM  12446  SG  CYS K  51      50.512  68.670  45.375  1.00137.26           S
  ATOM  12470  SG  CYS K  54      52.924  69.743  42.642  1.00135.51           S
  ATOM  12187  SG  CYS K  16      41.580  66.180  52.218  1.00144.97           S
  ATOM  12205  SG  CYS K  19      40.762  63.036  54.186  1.00143.14           S
  ATOM  12335  SG  CYS K  36      43.515  65.426  55.432  1.00132.02           S
  ATOM  12357  SG  CYS K  39      43.985  63.037  52.593  1.00138.90           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.55, per 1000 atoms: 0.24
  Number of scatterers: 14591
  At special positions: 0
  Unit cell: (128.816, 130.144, 124.832, 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      33     16.00
     P     294     15.00
     O    3288      8.00
     N    2710      7.00
     C    8264      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: 1.23
  Conformation dependent library (CDL) restraints added in 486.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      62.7% alpha, 5.4% beta
      135 base pairs and 239 stacking pairs defined.
    Time for finding SS restraints: 2.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.593A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.561A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.868A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.647A  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: 3.614A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.613A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.558A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.716A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.716A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.647A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.936A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.721A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.526A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.635A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.530A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.695A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 68
      removed outlier: 3.533A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 4.279A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.596A  pdb=" N   ARG L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.582A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 3.884A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.796A  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 'B' and resid 96 through 98
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.784A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.362A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.520A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16
      removed outlier: 3.559A  pdb=" N   HIS M  68 " --> pdb=" O   ILE M  44 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      239 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 1.67 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: 3554
        1.34 -     1.46: 4330
        1.46 -     1.58: 6943
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15462
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.35e+00
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.547 -0.022 2.00e-02 2.50e+03 1.20e+00
  bond pdb=" CA  ASP B  24 "
       pdb=" CB  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.527  1.545 -0.018 1.70e-02 3.46e+03 1.15e+00
  bond pdb=" C4'  DT I -26 "
       pdb=" C3'  DT I -26 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 2.00e-02 2.50e+03 1.08e+00
  ... (remaining 15457 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 21726
        1.99 -     3.98: 400
        3.98 -     5.97: 27
        5.97 -     7.96: 1
        7.96 -     9.95: 2
  Bond angle restraints: 22156
  Sorted by residual:
  angle pdb=" C   TYR L  60 "
        pdb=" N   PRO L  61 "
        pdb=" CA  PRO L  61 "
      ideal   model   delta    sigma   weight residual
     127.00  136.95   -9.95 2.40e+00 1.74e-01 1.72e+01
  angle pdb=" C   TYR L  60 "
        pdb=" N   PRO L  61 "
        pdb=" CD  PRO L  61 "
      ideal   model   delta    sigma   weight residual
     120.60  112.27    8.33 2.20e+00 2.07e-01 1.43e+01
  angle pdb=" CA  ARG K  86 "
        pdb=" CB  ARG K  86 "
        pdb=" CG  ARG K  86 "
      ideal   model   delta    sigma   weight residual
     114.10  119.75   -5.65 2.00e+00 2.50e-01 7.99e+00
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.46  126.40   -3.94 1.41e+00 5.03e-01 7.80e+00
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.58   -3.98 1.50e+00 4.44e-01 7.05e+00
  ... (remaining 22151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 7269
       35.45 -    70.90: 1314
       70.90 -   106.36: 17
      106.36 -   141.81: 0
      141.81 -   177.26: 2
  Dihedral angle restraints: 8602
    sinusoidal: 5466
      harmonic: 3136
  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
    -140.00   37.26 -177.26     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   72.91  147.09     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" CG  ARG A 128 "
           pdb=" CD  ARG A 128 "
           pdb=" NE  ARG A 128 "
           pdb=" CZ  ARG A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.54   43.54     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 8599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1731
       0.030 -    0.061: 587
       0.061 -    0.091: 128
       0.091 -    0.121: 60
       0.121 -    0.151: 8
  Chirality restraints: 2514
  Sorted by residual:
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  ARG L 136 "
            pdb=" N   ARG L 136 "
            pdb=" C   ARG L 136 "
            pdb=" CB  ARG L 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" CA  PRO E 121 "
            pdb=" N   PRO E 121 "
            pdb=" C   PRO E 121 "
            pdb=" CB  PRO E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 2511 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.025 2.00e-02 2.50e+03   1.05e-02 3.33e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.024 2.00e-02 2.50e+03   1.02e-02 2.84e+00
        pdb=" N9   DA I -35 "    0.020 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO G  80 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 414
        2.68 -     3.24: 13010
        3.24 -     3.79: 26178
        3.79 -     4.35: 32343
        4.35 -     4.90: 47562
  Nonbonded interactions: 119507
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU K  45 "
            pdb=" NZ  LYS K  46 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.138 2.496
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" NH1 ARG K  63 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   PRO L  40 "
            pdb=" OG  SER L  43 "
     model   vdw
     2.222 3.040
  ... (remaining 119502 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
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 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     18.700
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
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      :  0.004   0.035  15472  Z= 0.173
  Angle     :  0.591   9.951  22171  Z= 0.342
  Chirality :  0.035   0.151   2514
  Planarity :  0.004   0.058   1792
  Dihedral  : 25.679 177.259   6570
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.27), residues: 1056
  helix:  2.26 (0.21), residues: 639
  sheet:  0.73 (0.81), residues: 48
  loop : -0.45 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG K  86 
 TYR   0.023   0.002   TYR H  40 
 PHE   0.007   0.001   PHE L  62 
 TRP   0.017   0.002   TRP L  33 
 HIS   0.004   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (15462)
  covalent geometry    : angle       0.58555 (22156)
  hydrogen bonds       : bond        0.10479 (  846)
  hydrogen bonds       : angle       4.29032 ( 2152)
  metal coordination   : bond        0.00789 (    8)
  metal coordination   : angle       4.14638 (    9)
  link_TRANS           : bond        0.00231 (    2)
  link_TRANS           : angle       0.35621 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 SER cc_start: 0.7819 (m) cc_final: 0.7514 (p)
REVERT: C   75 LYS cc_start: 0.9250 (mmtp) cc_final: 0.8951 (mmmm)
REVERT: C  111 ILE cc_start: 0.9141 (mt) cc_final: 0.8918 (tt)
REVERT: D   33 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7930 (mtp-110)
REVERT: D   59 MET cc_start: 0.9391 (tpp) cc_final: 0.8980 (tpp)
REVERT: D  116 LYS cc_start: 0.9335 (tmtt) cc_final: 0.8991 (tttp)
REVERT: E   94 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7904 (mm-30)
REVERT: G   39 TYR cc_start: 0.8796 (m-80) cc_final: 0.8454 (m-80)
REVERT: G   56 GLU cc_start: 0.8353 (tt0) cc_final: 0.7968 (tt0)
REVERT: G   84 GLN cc_start: 0.9562 (tp-100) cc_final: 0.9354 (tp-100)
REVERT: H  120 LYS cc_start: 0.9184 (tttm) cc_final: 0.8906 (ttmt)
REVERT: K   39 CYS cc_start: 0.3631 (m) cc_final: 0.2810 (m)
REVERT: L   86 LEU cc_start: 0.8696 (tp) cc_final: 0.8403 (tp)
REVERT: L   97 LEU cc_start: 0.8363 (mt) cc_final: 0.8085 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1489
  time to fit residues: 51.3390
Evaluate side-chains
  193 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
E  68 GLN
E 108 ASN
F  25 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.116792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.077766 restraints weight = 47625.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.077557 restraints weight = 38707.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.077625 restraints weight = 42081.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.077881 restraints weight = 26152.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.078620 restraints weight = 22716.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  15472  Z= 0.255
  Angle     :  0.657  15.395  22171  Z= 0.366
  Chirality :  0.038   0.161   2514
  Planarity :  0.005   0.043   1792
  Dihedral  : 28.891 176.456   4410
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.81 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.27), residues: 1056
  helix:  2.06 (0.21), residues: 657
  sheet:  0.61 (0.81), residues: 48
  loop : -0.70 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  33 
 TYR   0.027   0.002   TYR B  88 
 PHE   0.010   0.002   PHE H  70 
 TRP   0.011   0.002   TRP L  33 
 HIS   0.006   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (15462)
  covalent geometry    : angle       0.63780 (22156)
  hydrogen bonds       : bond        0.05268 (  846)
  hydrogen bonds       : angle       3.82658 ( 2152)
  metal coordination   : bond        0.00969 (    8)
  metal coordination   : angle       7.75549 (    9)
  link_TRANS           : bond        0.00314 (    2)
  link_TRANS           : angle       0.49232 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8528 (pp30) cc_final: 0.8291 (pp30)
REVERT: A   93 GLN cc_start: 0.9020 (tt0) cc_final: 0.8805 (tt0)
REVERT: B   59 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8566 (ttmm)
REVERT: B   88 TYR cc_start: 0.8355 (m-10) cc_final: 0.6861 (m-10)
REVERT: C   18 SER cc_start: 0.8021 (m) cc_final: 0.7775 (p)
REVERT: C   75 LYS cc_start: 0.9233 (mmtp) cc_final: 0.9032 (mmtp)
REVERT: D   59 MET cc_start: 0.9446 (tpp) cc_final: 0.9075 (tpp)
REVERT: E   94 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8045 (mm-30)
REVERT: F   74 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8246 (mm-30)
REVERT: G   56 GLU cc_start: 0.8289 (tt0) cc_final: 0.7949 (tt0)
REVERT: H   57 LYS cc_start: 0.8348 (mmmm) cc_final: 0.8121 (mmmm)
REVERT: H   71 GLU cc_start: 0.8582 (tp30) cc_final: 0.8320 (tp30)
REVERT: H  120 LYS cc_start: 0.9114 (tttm) cc_final: 0.8845 (ttmt)
REVERT: K   35 LEU cc_start: 0.7276 (tp) cc_final: 0.6475 (tp)
REVERT: K   46 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7854 (mtmm)
REVERT: L   97 LEU cc_start: 0.8405 (mt) cc_final: 0.8117 (mt)
  outliers start: 19
  outliers final: 14
  residues processed: 212
  average time/residue: 0.1502
  time to fit residues: 44.4010
Evaluate side-chains
  196 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain M residue    5 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 106 optimal weight:    9.9990
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 128 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 100 optimal weight:   20.0000
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
H  49 HIS
L   7 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.119278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.080175 restraints weight = 48076.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.080003 restraints weight = 38406.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.080243 restraints weight = 41084.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.080387 restraints weight = 26290.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.081225 restraints weight = 22960.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  15472  Z= 0.159
  Angle     :  0.591  12.228  22171  Z= 0.335
  Chirality :  0.035   0.178   2514
  Planarity :  0.004   0.044   1792
  Dihedral  : 28.888 176.504   4410
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.85 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.27), residues: 1056
  helix:  2.31 (0.21), residues: 650
  sheet:  0.63 (0.75), residues: 49
  loop : -0.61 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG M  54 
 TYR   0.029   0.002   TYR H  83 
 PHE   0.010   0.001   PHE M   4 
 TRP   0.012   0.001   TRP L  33 
 HIS   0.003   0.001   HIS L  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (15462)
  covalent geometry    : angle       0.57799 (22156)
  hydrogen bonds       : bond        0.04250 (  846)
  hydrogen bonds       : angle       3.40940 ( 2152)
  metal coordination   : bond        0.02083 (    8)
  metal coordination   : angle       6.06486 (    9)
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.30740 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8805 (tt0) cc_final: 0.8574 (tt0)
REVERT: B   88 TYR cc_start: 0.7870 (m-10) cc_final: 0.7278 (m-10)
REVERT: C   18 SER cc_start: 0.8162 (m) cc_final: 0.7883 (p)
REVERT: C   29 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7762 (ttm170)
REVERT: D   35 GLU cc_start: 0.8459 (tp30) cc_final: 0.7751 (mm-30)
REVERT: D   59 MET cc_start: 0.9414 (tpp) cc_final: 0.9049 (tpp)
REVERT: D  119 THR cc_start: 0.9302 (t) cc_final: 0.9091 (t)
REVERT: E   94 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8029 (mm-30)
REVERT: E  125 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7549 (mm-40)
REVERT: G   56 GLU cc_start: 0.8364 (tt0) cc_final: 0.7913 (tt0)
REVERT: G   84 GLN cc_start: 0.9629 (tp-100) cc_final: 0.9402 (tp-100)
REVERT: H   71 GLU cc_start: 0.8664 (tp30) cc_final: 0.8425 (tp30)
REVERT: H  120 LYS cc_start: 0.9112 (tttm) cc_final: 0.8895 (ttmt)
REVERT: K   68 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7272 (mtt180)
REVERT: L  147 MET cc_start: 0.6883 (tpt) cc_final: 0.6159 (tpp)
  outliers start: 20
  outliers final: 12
  residues processed: 223
  average time/residue: 0.1506
  time to fit residues: 46.8533
Evaluate side-chains
  212 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 199
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   chunk 127 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 125 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
K  15 GLN
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.118220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.068588 restraints weight = 53742.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.070228 restraints weight = 28205.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.070989 restraints weight = 17726.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.071502 restraints weight = 15506.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.071309 restraints weight = 14440.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15472  Z= 0.193
  Angle     :  0.600  12.516  22171  Z= 0.338
  Chirality :  0.035   0.180   2514
  Planarity :  0.004   0.042   1792
  Dihedral  : 28.942 176.069   4410
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.83 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.26), residues: 1056
  helix:  2.25 (0.21), residues: 650
  sheet:  0.04 (0.69), residues: 44
  loop : -0.69 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  33 
 TYR   0.035   0.002   TYR D  83 
 PHE   0.009   0.001   PHE G  25 
 TRP   0.015   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (15462)
  covalent geometry    : angle       0.59028 (22156)
  hydrogen bonds       : bond        0.04554 (  846)
  hydrogen bonds       : angle       3.53963 ( 2152)
  metal coordination   : bond        0.01515 (    8)
  metal coordination   : angle       5.36788 (    9)
  link_TRANS           : bond        0.00134 (    2)
  link_TRANS           : angle       0.42115 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9080 (tt0) cc_final: 0.8838 (tt0)
REVERT: C   18 SER cc_start: 0.8508 (m) cc_final: 0.8289 (p)
REVERT: C   29 ARG cc_start: 0.8526 (ttm170) cc_final: 0.7916 (ttm170)
REVERT: D   35 GLU cc_start: 0.8507 (tp30) cc_final: 0.7794 (mm-30)
REVERT: D   59 MET cc_start: 0.9404 (tpp) cc_final: 0.8930 (tpp)
REVERT: D  119 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9104 (t)
REVERT: E   94 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: G   56 GLU cc_start: 0.8513 (tt0) cc_final: 0.8121 (tt0)
REVERT: G   84 GLN cc_start: 0.9542 (tp-100) cc_final: 0.9246 (tp-100)
REVERT: H   57 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8380 (mmmm)
REVERT: H   71 GLU cc_start: 0.8755 (tp30) cc_final: 0.8509 (tp30)
REVERT: H  120 LYS cc_start: 0.9123 (tttm) cc_final: 0.8876 (ttmt)
REVERT: K   35 LEU cc_start: 0.7142 (tp) cc_final: 0.6902 (tt)
REVERT: K   46 LYS cc_start: 0.8176 (mttt) cc_final: 0.7520 (mtmm)
REVERT: L   66 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8254 (mmtm)
REVERT: M   52 ASP cc_start: 0.8193 (m-30) cc_final: 0.7838 (t0)
  outliers start: 20
  outliers final: 10
  residues processed: 209
  average time/residue: 0.1478
  time to fit residues: 43.2371
Evaluate side-chains
  202 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 191
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 104 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 119 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
K  15 GLN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.119797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.071282 restraints weight = 62841.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.072974 restraints weight = 31027.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.074164 restraints weight = 19299.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.074153 restraints weight = 17624.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.073852 restraints weight = 14279.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15472  Z= 0.155
  Angle     :  0.579  12.796  22171  Z= 0.327
  Chirality :  0.034   0.195   2514
  Planarity :  0.004   0.043   1792
  Dihedral  : 28.916 176.298   4410
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.26 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.26), residues: 1056
  helix:  2.35 (0.21), residues: 649
  sheet: -0.05 (0.69), residues: 43
  loop : -0.69 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  33 
 TYR   0.034   0.002   TYR D  83 
 PHE   0.009   0.001   PHE M   4 
 TRP   0.014   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (15462)
  covalent geometry    : angle       0.56997 (22156)
  hydrogen bonds       : bond        0.04087 (  846)
  hydrogen bonds       : angle       3.35804 ( 2152)
  metal coordination   : bond        0.01375 (    8)
  metal coordination   : angle       5.19281 (    9)
  link_TRANS           : bond        0.00035 (    2)
  link_TRANS           : angle       0.38812 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8931 (tt0) cc_final: 0.8683 (tt0)
REVERT: B   88 TYR cc_start: 0.7781 (m-10) cc_final: 0.7470 (m-10)
REVERT: C   18 SER cc_start: 0.8410 (m) cc_final: 0.8201 (p)
REVERT: C   29 ARG cc_start: 0.8429 (ttm170) cc_final: 0.7806 (ttm170)
REVERT: D   35 GLU cc_start: 0.8415 (tp30) cc_final: 0.7716 (mm-30)
REVERT: D   59 MET cc_start: 0.9376 (tpp) cc_final: 0.8960 (tpp)
REVERT: D   85 LYS cc_start: 0.9297 (mtmm) cc_final: 0.8956 (mtmm)
REVERT: D  119 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9052 (t)
REVERT: E   94 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7929 (mm-30)
REVERT: G   56 GLU cc_start: 0.8593 (tt0) cc_final: 0.8227 (tt0)
REVERT: G   84 GLN cc_start: 0.9558 (tp-100) cc_final: 0.9337 (tp-100)
REVERT: H   71 GLU cc_start: 0.8681 (tp30) cc_final: 0.8424 (tp30)
REVERT: H  120 LYS cc_start: 0.9040 (tttm) cc_final: 0.8787 (ttmt)
REVERT: L   66 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8394 (mmtm)
REVERT: L  136 ARG cc_start: 0.9648 (OUTLIER) cc_final: 0.9432 (ttp80)
REVERT: M   25 ASN cc_start: 0.9492 (t0) cc_final: 0.9289 (t0)
REVERT: M   52 ASP cc_start: 0.8307 (m-30) cc_final: 0.7487 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 208
  average time/residue: 0.1483
  time to fit residues: 43.2687
Evaluate side-chains
  202 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 110 optimal weight:    8.9990
   chunk 128 optimal weight:   20.0000
   chunk 7 optimal weight:    0.7980
   chunk 100 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 112 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.118435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.066497 restraints weight = 62529.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.069664 restraints weight = 33296.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.069794 restraints weight = 20756.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.069961 restraints weight = 17701.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.070116 restraints weight = 16965.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  15472  Z= 0.200
  Angle     :  0.614  12.723  22171  Z= 0.342
  Chirality :  0.035   0.190   2514
  Planarity :  0.004   0.047   1792
  Dihedral  : 28.970 175.813   4410
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.16 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.26), residues: 1056
  helix:  2.29 (0.21), residues: 649
  sheet: -0.18 (0.65), residues: 43
  loop : -0.74 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  33 
 TYR   0.027   0.002   TYR D  83 
 PHE   0.008   0.001   PHE B  61 
 TRP   0.013   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (15462)
  covalent geometry    : angle       0.59890 (22156)
  hydrogen bonds       : bond        0.04596 (  846)
  hydrogen bonds       : angle       3.51449 ( 2152)
  metal coordination   : bond        0.01484 (    8)
  metal coordination   : angle       6.82272 (    9)
  link_TRANS           : bond        0.00155 (    2)
  link_TRANS           : angle       0.46706 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9087 (tt0) cc_final: 0.8826 (tt0)
REVERT: B   88 TYR cc_start: 0.7920 (m-10) cc_final: 0.7305 (m-10)
REVERT: C   18 SER cc_start: 0.8486 (m) cc_final: 0.8261 (p)
REVERT: C   29 ARG cc_start: 0.8510 (ttm170) cc_final: 0.7833 (ttm170)
REVERT: D   35 GLU cc_start: 0.8389 (tp30) cc_final: 0.7662 (mm-30)
REVERT: D   59 MET cc_start: 0.9456 (tpp) cc_final: 0.9047 (tpp)
REVERT: D   85 LYS cc_start: 0.9319 (mtmm) cc_final: 0.8987 (mtmm)
REVERT: D  119 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9111 (t)
REVERT: E   94 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8012 (mm-30)
REVERT: G   56 GLU cc_start: 0.8619 (tt0) cc_final: 0.8195 (tt0)
REVERT: G   84 GLN cc_start: 0.9521 (tp-100) cc_final: 0.9253 (tp-100)
REVERT: H   71 GLU cc_start: 0.8724 (tp30) cc_final: 0.8484 (tp30)
REVERT: H  120 LYS cc_start: 0.9058 (tttm) cc_final: 0.8789 (ttmt)
REVERT: K   35 LEU cc_start: 0.6957 (tp) cc_final: 0.6736 (tt)
REVERT: L    5 ARG cc_start: 0.8565 (tmt-80) cc_final: 0.8054 (tmt170)
REVERT: L   30 MET cc_start: 0.8940 (tpp) cc_final: 0.8731 (tpp)
REVERT: L   66 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8387 (mmtm)
REVERT: M   27 LYS cc_start: 0.9531 (ptmm) cc_final: 0.9325 (pttp)
  outliers start: 25
  outliers final: 19
  residues processed: 209
  average time/residue: 0.1382
  time to fit residues: 40.8255
Evaluate side-chains
  205 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 104 optimal weight:    7.9990
   chunk 128 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
L  46 GLN
M  25 ASN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.119916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.069631 restraints weight = 54008.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.071603 restraints weight = 31862.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.072352 restraints weight = 20110.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.072669 restraints weight = 17154.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.072833 restraints weight = 16686.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15472  Z= 0.161
  Angle     :  0.608  13.068  22171  Z= 0.335
  Chirality :  0.035   0.205   2514
  Planarity :  0.004   0.048   1792
  Dihedral  : 28.927 176.167   4410
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.57 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.26), residues: 1056
  helix:  2.32 (0.21), residues: 650
  sheet: -0.35 (0.64), residues: 44
  loop : -0.64 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  33 
 TYR   0.023   0.002   TYR H  40 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.011   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (15462)
  covalent geometry    : angle       0.59258 (22156)
  hydrogen bonds       : bond        0.04118 (  846)
  hydrogen bonds       : angle       3.36397 ( 2152)
  metal coordination   : bond        0.01046 (    8)
  metal coordination   : angle       6.71041 (    9)
  link_TRANS           : bond        0.00054 (    2)
  link_TRANS           : angle       0.40758 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 197
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8946 (tt0) cc_final: 0.8688 (tt0)
REVERT: B   88 TYR cc_start: 0.7915 (m-10) cc_final: 0.7176 (m-10)
REVERT: C   18 SER cc_start: 0.8200 (m) cc_final: 0.7995 (p)
REVERT: D   35 GLU cc_start: 0.8398 (tp30) cc_final: 0.7865 (mm-30)
REVERT: D   59 MET cc_start: 0.9394 (tpp) cc_final: 0.8983 (tpp)
REVERT: D   85 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8968 (mtmm)
REVERT: D  119 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.9043 (t)
REVERT: E   94 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7983 (mm-30)
REVERT: G   56 GLU cc_start: 0.8480 (tt0) cc_final: 0.8033 (tt0)
REVERT: H   59 MET cc_start: 0.9152 (tpt) cc_final: 0.8908 (tpp)
REVERT: H   71 GLU cc_start: 0.8680 (tp30) cc_final: 0.8451 (tp30)
REVERT: H  120 LYS cc_start: 0.9035 (tttm) cc_final: 0.8758 (ttmt)
REVERT: L    5 ARG cc_start: 0.8541 (tmt-80) cc_final: 0.8056 (tmt170)
REVERT: L   30 MET cc_start: 0.8817 (tpp) cc_final: 0.8582 (tpp)
REVERT: L   66 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8388 (mppt)
REVERT: M   24 GLU cc_start: 0.9135 (mp0) cc_final: 0.8722 (mp0)
REVERT: M   27 LYS cc_start: 0.9594 (ptmm) cc_final: 0.9358 (pttp)
  outliers start: 22
  outliers final: 19
  residues processed: 205
  average time/residue: 0.1430
  time to fit residues: 41.5211
Evaluate side-chains
  205 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Chi-restraints excluded: chain M residue   25 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 110 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 104 optimal weight:   10.0000
   chunk 121 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.120027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.076151 restraints weight = 37160.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.076453 restraints weight = 26342.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.076449 restraints weight = 23253.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.076773 restraints weight = 20023.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.076987 restraints weight = 17894.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15472  Z= 0.157
  Angle     :  0.598  13.358  22171  Z= 0.333
  Chirality :  0.035   0.214   2514
  Planarity :  0.004   0.053   1792
  Dihedral  : 28.914 176.122   4410
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.98 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.26), residues: 1056
  helix:  2.37 (0.21), residues: 650
  sheet: -0.20 (0.66), residues: 44
  loop : -0.66 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D  33 
 TYR   0.021   0.001   TYR H  40 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.010   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (15462)
  covalent geometry    : angle       0.58663 (22156)
  hydrogen bonds       : bond        0.04078 (  846)
  hydrogen bonds       : angle       3.34228 ( 2152)
  metal coordination   : bond        0.01820 (    8)
  metal coordination   : angle       5.73534 (    9)
  link_TRANS           : bond        0.00033 (    2)
  link_TRANS           : angle       0.39854 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.7890 (m-10) cc_final: 0.7032 (m-10)
REVERT: C   18 SER cc_start: 0.7983 (m) cc_final: 0.7735 (p)
REVERT: D   59 MET cc_start: 0.9346 (tpp) cc_final: 0.8929 (tpp)
REVERT: D   85 LYS cc_start: 0.9315 (mtmm) cc_final: 0.8988 (mtmm)
REVERT: E   94 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: G   56 GLU cc_start: 0.8537 (tt0) cc_final: 0.8137 (tt0)
REVERT: G   57 TYR cc_start: 0.9092 (t80) cc_final: 0.8867 (t80)
REVERT: H   59 MET cc_start: 0.9113 (tpt) cc_final: 0.8840 (tpp)
REVERT: H   71 GLU cc_start: 0.8695 (tp30) cc_final: 0.8459 (tp30)
REVERT: H  120 LYS cc_start: 0.9017 (tttm) cc_final: 0.8767 (ttmt)
REVERT: L   30 MET cc_start: 0.8190 (tpp) cc_final: 0.7982 (tpp)
REVERT: L   66 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8243 (mppt)
REVERT: M   24 GLU cc_start: 0.8704 (mp0) cc_final: 0.8243 (mp0)
REVERT: M   52 ASP cc_start: 0.6754 (m-30) cc_final: 0.6223 (t0)
  outliers start: 24
  outliers final: 20
  residues processed: 206
  average time/residue: 0.1385
  time to fit residues: 40.8529
Evaluate side-chains
  205 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 113 optimal weight:   30.0000
   chunk 119 optimal weight:    0.0470
   chunk 54 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.8880

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.119914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.079524 restraints weight = 44728.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.078311 restraints weight = 35289.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.079542 restraints weight = 29323.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.079648 restraints weight = 22643.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.080063 restraints weight = 22888.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  15472  Z= 0.166
  Angle     :  0.603  13.439  22171  Z= 0.336
  Chirality :  0.035   0.217   2514
  Planarity :  0.004   0.055   1792
  Dihedral  : 28.914 175.933   4410
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.98 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.26), residues: 1056
  helix:  2.36 (0.21), residues: 650
  sheet: -0.18 (0.64), residues: 43
  loop : -0.63 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  33 
 TYR   0.021   0.002   TYR H  40 
 PHE   0.008   0.001   PHE H  70 
 TRP   0.009   0.001   TRP L  33 
 HIS   0.004   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (15462)
  covalent geometry    : angle       0.59373 (22156)
  hydrogen bonds       : bond        0.04175 (  846)
  hydrogen bonds       : angle       3.34294 ( 2152)
  metal coordination   : bond        0.02066 (    8)
  metal coordination   : angle       5.25333 (    9)
  link_TRANS           : bond        0.00058 (    2)
  link_TRANS           : angle       0.41860 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8795 (tt0) cc_final: 0.8549 (tt0)
REVERT: B   88 TYR cc_start: 0.7969 (m-10) cc_final: 0.7257 (m-10)
REVERT: D   35 GLU cc_start: 0.8400 (tp30) cc_final: 0.7793 (mm-30)
REVERT: D   59 MET cc_start: 0.9393 (tpp) cc_final: 0.9065 (tpp)
REVERT: D   85 LYS cc_start: 0.9278 (mtmm) cc_final: 0.8966 (mtmm)
REVERT: G   56 GLU cc_start: 0.8484 (tt0) cc_final: 0.8067 (tt0)
REVERT: G   57 TYR cc_start: 0.9103 (t80) cc_final: 0.8867 (t80)
REVERT: H   59 MET cc_start: 0.8975 (tpt) cc_final: 0.8747 (tpp)
REVERT: H   71 GLU cc_start: 0.8635 (tp30) cc_final: 0.8359 (tp30)
REVERT: H  120 LYS cc_start: 0.8999 (tttm) cc_final: 0.8752 (ttmt)
REVERT: L   30 MET cc_start: 0.8212 (tpp) cc_final: 0.8008 (tpp)
REVERT: L   66 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8224 (mppt)
REVERT: M   24 GLU cc_start: 0.8650 (mp0) cc_final: 0.8179 (mp0)
REVERT: M   52 ASP cc_start: 0.6714 (m-30) cc_final: 0.6210 (t0)
  outliers start: 21
  outliers final: 20
  residues processed: 202
  average time/residue: 0.1351
  time to fit residues: 39.2547
Evaluate side-chains
  204 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain K residue   86 ARG
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 121 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  55 HIS
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.119802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.080213 restraints weight = 47259.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.080866 restraints weight = 39587.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.080531 restraints weight = 43736.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.080849 restraints weight = 26302.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.081499 restraints weight = 23138.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15472  Z= 0.177
  Angle     :  0.615  14.157  22171  Z= 0.343
  Chirality :  0.035   0.222   2514
  Planarity :  0.004   0.060   1792
  Dihedral  : 28.926 175.784   4410
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.63 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1056
  helix:  2.33 (0.21), residues: 649
  sheet: -0.20 (0.64), residues: 43
  loop : -0.64 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  33 
 TYR   0.021   0.002   TYR H  40 
 PHE   0.008   0.001   PHE H  70 
 TRP   0.009   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (15462)
  covalent geometry    : angle       0.60531 (22156)
  hydrogen bonds       : bond        0.04283 (  846)
  hydrogen bonds       : angle       3.41803 ( 2152)
  metal coordination   : bond        0.01601 (    8)
  metal coordination   : angle       5.37443 (    9)
  link_TRANS           : bond        0.00079 (    2)
  link_TRANS           : angle       0.43894 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8839 (tt0) cc_final: 0.8598 (tt0)
REVERT: B   88 TYR cc_start: 0.7778 (m-10) cc_final: 0.7045 (m-10)
REVERT: D   59 MET cc_start: 0.9322 (tpp) cc_final: 0.8973 (tpp)
REVERT: D   85 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8961 (mtmm)
REVERT: G   56 GLU cc_start: 0.8515 (tt0) cc_final: 0.8071 (tt0)
REVERT: G   57 TYR cc_start: 0.9123 (t80) cc_final: 0.8880 (t80)
REVERT: H   59 MET cc_start: 0.8951 (tpt) cc_final: 0.8728 (tpp)
REVERT: H   71 GLU cc_start: 0.8627 (tp30) cc_final: 0.8351 (tp30)
REVERT: H  120 LYS cc_start: 0.8959 (tttm) cc_final: 0.8729 (ttmt)
REVERT: L   30 MET cc_start: 0.8143 (tpp) cc_final: 0.7923 (tpp)
REVERT: L   66 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8242 (mppt)
REVERT: M   24 GLU cc_start: 0.8547 (mp0) cc_final: 0.8136 (mp0)
REVERT: M   52 ASP cc_start: 0.6409 (m-30) cc_final: 0.6002 (t0)
  outliers start: 21
  outliers final: 21
  residues processed: 198
  average time/residue: 0.1277
  time to fit residues: 36.1943
Evaluate side-chains
  203 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain K residue   86 ARG
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 126 optimal weight:   30.0000
   chunk 23 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 128 optimal weight:    6.9990
   chunk 125 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.120303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.080717 restraints weight = 46017.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.080856 restraints weight = 39196.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.080818 restraints weight = 42981.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.081002 restraints weight = 26343.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.081377 restraints weight = 23052.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15472  Z= 0.164
  Angle     :  0.615  14.065  22171  Z= 0.343
  Chirality :  0.035   0.222   2514
  Planarity :  0.004   0.058   1792
  Dihedral  : 28.920 175.970   4410
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.28 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.26), residues: 1056
  helix:  2.35 (0.21), residues: 649
  sheet: -0.45 (0.66), residues: 42
  loop : -0.62 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  33 
 TYR   0.021   0.001   TYR H  40 
 PHE   0.016   0.001   PHE M   4 
 TRP   0.007   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (15462)
  covalent geometry    : angle       0.60612 (22156)
  hydrogen bonds       : bond        0.04180 (  846)
  hydrogen bonds       : angle       3.37756 ( 2152)
  metal coordination   : bond        0.01347 (    8)
  metal coordination   : angle       5.21136 (    9)
  link_TRANS           : bond        0.00038 (    2)
  link_TRANS           : angle       0.42180 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2489.71 seconds
wall clock time: 43 minutes 38.92 seconds (2618.92 seconds total)