Starting phenix.real_space_refine
on Fri May 16 09:15:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn8_40616/05_2025/8sn8_40616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn8_40616/05_2025/8sn8_40616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn8_40616/05_2025/8sn8_40616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn8_40616/05_2025/8sn8_40616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn8_40616/05_2025/8sn8_40616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn8_40616/05_2025/8sn8_40616.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14600
  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: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "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      34.250  72.890  43.549  1.00 74.78           S
  ATOM  12446  SG  CYS K  51      31.943  69.964  43.371  1.00 65.34           S
  ATOM  12470  SG  CYS K  54      34.443  70.787  40.404  1.00 80.92           S
  ATOM  12187  SG  CYS K  16      21.836  69.400  49.197  1.00 88.95           S
  ATOM  12205  SG  CYS K  19      19.480  67.747  51.492  1.00 90.04           S
  ATOM  12335  SG  CYS K  36      22.401  69.913  52.882  1.00 73.23           S
  ATOM  12357  SG  CYS K  39      23.142  66.555  51.678  1.00 76.19           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: 8.70, per 1000 atoms: 0.60
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (110.224, 132.8, 127.488, 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    3289      8.00
     N    2713      7.00
     C    8269      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.27
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 13 sheets defined
      62.6% alpha, 5.3% beta
      135 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 5.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.546A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.556A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.912A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.848A  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 45 through 73
      removed outlier: 4.710A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.693A  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: 3.542A  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: 3.578A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.545A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.685A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.796A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.960A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.598A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    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
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.805A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.729A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 3.667A  pdb=" N   SER K  42 " --> pdb=" O   PRO K  38 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL K  44 " --> pdb=" O   PHE K  40 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS K  46 " --> pdb=" O   SER K  42 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.800A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.576A  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: 4.054A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.586A  pdb=" N   ASP L  16 " --> pdb=" O   ASP L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 4.267A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER L  91 " --> pdb=" O   ASP L  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 86 through 91'
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.642A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.530A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 147
      removed outlier: 3.550A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS L 144 " --> pdb=" O   GLU L 140 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   MET L 147 " --> pdb=" O   GLN L 143 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    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: 6.862A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.878A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.789A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.187A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.737A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16

    492 hydrogen bonds defined for protein.
    1446 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 4.78

  Time building geometry restraints manager: 3.87 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: 3565
        1.34 -     1.46: 4321
        1.46 -     1.58: 6951
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" CB  ARG K  55 "
       pdb=" CG  ARG K  55 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CB  ASP E  81 "
       pdb=" CG  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.13e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CA  ASP E  81 "
       pdb=" CB  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 9.68e-01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.90e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 21683
        1.65 -     3.31: 447
        3.31 -     4.96: 30
        4.96 -     6.62: 8
        6.62 -     8.27: 3
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  120.97   -8.27 3.00e+00 1.11e-01 7.60e+00
  angle pdb=" C   THR E  80 "
        pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     121.54  126.55   -5.01 1.91e+00 2.74e-01 6.88e+00
  angle pdb=" CB  MET D  59 "
        pdb=" CG  MET D  59 "
        pdb=" SD  MET D  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.03    7.67 3.00e+00 1.11e-01 6.53e+00
  angle pdb=" C   ALA L  14 "
        pdb=" N   ARG L  15 "
        pdb=" CA  ARG L  15 "
      ideal   model   delta    sigma   weight residual
     121.58  117.14    4.44 1.95e+00 2.63e-01 5.19e+00
  angle pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
        pdb=" C   ASP E  81 "
      ideal   model   delta    sigma   weight residual
     110.80  115.63   -4.83 2.13e+00 2.20e-01 5.13e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.54: 7276
       35.54 -    71.07: 1315
       71.07 -   106.61: 18
      106.61 -   142.14: 0
      142.14 -   177.68: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  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   37.68 -177.68     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   74.80  145.20     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" CA  PHE K  53 "
           pdb=" C   PHE K  53 "
           pdb=" N   CYS K  54 "
           pdb=" CA  CYS K  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.65  -18.35     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1919
       0.035 -    0.069: 450
       0.069 -    0.104: 110
       0.104 -    0.138: 35
       0.138 -    0.173: 2
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.49e-01
  chirality pdb=" CB  ILE D  94 "
            pdb=" CA  ILE D  94 "
            pdb=" CG1 ILE D  94 "
            pdb=" CG2 ILE D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  GLU K  25 "
            pdb=" N   GLU K  25 "
            pdb=" C   GLU K  25 "
            pdb=" CB  GLU K  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG K  55 "    0.146 9.50e-02 1.11e+02   6.56e-02 2.79e+00
        pdb=" NE  ARG K  55 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG K  55 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG K  55 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG K  55 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO D 103 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K  37 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO K  38 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO K  38 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO K  38 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 865
        2.73 -     3.27: 13390
        3.27 -     3.81: 26953
        3.81 -     4.36: 31182
        4.36 -     4.90: 47064
  Nonbonded interactions: 119454
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.185 2.496
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OH  TYR H  40 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NZ  LYS M  63 "
            pdb=" OE2 GLU M  64 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG1 THR M  22 "
            pdb=" OE1 GLU M  24 "
     model   vdw
     2.276 3.040
  ... (remaining 119449 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=0.17 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     38.490
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15482  Z= 0.149
  Angle     :  0.553   8.271  22186  Z= 0.318
  Chirality :  0.034   0.173   2516
  Planarity :  0.004   0.066   1794
  Dihedral  : 25.620 177.679   6577
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.26), residues: 1057
  helix:  2.45 (0.21), residues: 629
  sheet:  1.04 (0.72), residues: 50
  loop : -0.47 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.014   0.001   PHE M   4 
 TYR   0.018   0.001   TYR H  40 
 ARG   0.007   0.000   ARG K  55 

Details of bonding type rmsd
  link_TRANS           : bond        0.00223 (    2)
  link_TRANS           : angle       0.46730 (    6)
  hydrogen bonds       : bond        0.11204 (  839)
  hydrogen bonds       : angle       3.88805 ( 2136)
  metal coordination   : bond        0.00814 (    8)
  metal coordination   : angle       4.88649 (    9)
  covalent geometry    : bond        0.00322 (15472)
  covalent geometry    : angle       0.54461 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8553 (ttmm)
REVERT: G   23 LEU cc_start: 0.9114 (mt) cc_final: 0.8768 (mt)
REVERT: G   76 THR cc_start: 0.9088 (p) cc_final: 0.8823 (t)
REVERT: G   78 ILE cc_start: 0.9207 (mm) cc_final: 0.8968 (mm)
REVERT: H  120 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8872 (tttp)
REVERT: L    3 LEU cc_start: 0.8855 (mm) cc_final: 0.8636 (mm)
REVERT: L   55 HIS cc_start: 0.7037 (m-70) cc_final: 0.6747 (m-70)
REVERT: M    1 MET cc_start: 0.3502 (ttt) cc_final: 0.1500 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.3551
  time to fit residues: 108.8121
Evaluate side-chains
  188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  83 HIS
L  32 HIS
** L  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.095825 restraints weight = 30683.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.094951 restraints weight = 40960.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.096391 restraints weight = 31767.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15482  Z= 0.192
  Angle     :  0.601  12.039  22186  Z= 0.337
  Chirality :  0.036   0.222   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 28.807 177.390   4413
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.96 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.26), residues: 1057
  helix:  2.27 (0.21), residues: 647
  sheet:  1.04 (0.71), residues: 50
  loop : -0.62 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP L  33 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.013   0.001   PHE M   4 
 TYR   0.019   0.002   TYR K  84 
 ARG   0.006   0.000   ARG A  53 

Details of bonding type rmsd
  link_TRANS           : bond        0.00141 (    2)
  link_TRANS           : angle       0.66134 (    6)
  hydrogen bonds       : bond        0.05137 (  839)
  hydrogen bonds       : angle       3.33653 ( 2136)
  metal coordination   : bond        0.01155 (    8)
  metal coordination   : angle       5.99888 (    9)
  covalent geometry    : bond        0.00439 (15472)
  covalent geometry    : angle       0.58881 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   83 TYR cc_start: 0.7835 (m-10) cc_final: 0.7623 (m-80)
REVERT: G   23 LEU cc_start: 0.9301 (mt) cc_final: 0.9012 (mt)
REVERT: G   76 THR cc_start: 0.9183 (p) cc_final: 0.8896 (t)
REVERT: G   78 ILE cc_start: 0.9371 (mm) cc_final: 0.9167 (mm)
REVERT: H   85 LYS cc_start: 0.8999 (mttp) cc_final: 0.8668 (mtmm)
REVERT: H  120 LYS cc_start: 0.9264 (ttmt) cc_final: 0.8963 (tttp)
REVERT: K   79 ILE cc_start: 0.8508 (mm) cc_final: 0.8263 (mm)
REVERT: L    8 LYS cc_start: 0.9018 (tptm) cc_final: 0.8698 (tptp)
REVERT: M    1 MET cc_start: 0.3446 (ttt) cc_final: 0.1420 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 203
  average time/residue: 0.3434
  time to fit residues: 93.8506
Evaluate side-chains
  198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 128 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 126 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 104 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.135107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.081143 restraints weight = 50151.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.083362 restraints weight = 29492.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.083380 restraints weight = 20513.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15482  Z= 0.191
  Angle     :  0.586  11.655  22186  Z= 0.330
  Chirality :  0.036   0.167   2516
  Planarity :  0.004   0.043   1794
  Dihedral  : 28.934 177.412   4413
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.69 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.26), residues: 1057
  helix:  2.22 (0.20), residues: 650
  sheet:  0.83 (0.69), residues: 50
  loop : -0.75 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP L  33 
 HIS   0.003   0.001   HIS L  55 
 PHE   0.011   0.001   PHE H  70 
 TYR   0.022   0.002   TYR H  40 
 ARG   0.004   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00053 (    2)
  link_TRANS           : angle       0.53785 (    6)
  hydrogen bonds       : bond        0.05121 (  839)
  hydrogen bonds       : angle       3.27194 ( 2136)
  metal coordination   : bond        0.01414 (    8)
  metal coordination   : angle       5.49161 (    9)
  covalent geometry    : bond        0.00439 (15472)
  covalent geometry    : angle       0.57602 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8767 (tpt) cc_final: 0.8480 (tpp)
REVERT: G   23 LEU cc_start: 0.9192 (mt) cc_final: 0.8856 (mt)
REVERT: G   76 THR cc_start: 0.9167 (p) cc_final: 0.8808 (t)
REVERT: G   78 ILE cc_start: 0.9393 (mm) cc_final: 0.9134 (mm)
REVERT: H   40 TYR cc_start: 0.8955 (m-80) cc_final: 0.8599 (m-10)
REVERT: H  120 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8956 (tttp)
REVERT: K   79 ILE cc_start: 0.8013 (mm) cc_final: 0.7719 (mm)
REVERT: L   33 TRP cc_start: 0.8759 (m100) cc_final: 0.8214 (m100)
  outliers start: 23
  outliers final: 19
  residues processed: 206
  average time/residue: 0.3543
  time to fit residues: 97.6416
Evaluate side-chains
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 72 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 103 optimal weight:    0.2980
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.135397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.080538 restraints weight = 44205.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.082419 restraints weight = 26213.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.083603 restraints weight = 19217.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15482  Z= 0.173
  Angle     :  0.577  11.317  22186  Z= 0.325
  Chirality :  0.035   0.169   2516
  Planarity :  0.004   0.042   1794
  Dihedral  : 28.972 177.571   4413
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.20 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1057
  helix:  2.29 (0.20), residues: 652
  sheet:  0.80 (0.69), residues: 50
  loop : -0.70 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L  33 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE H  70 
 TYR   0.019   0.001   TYR H  40 
 ARG   0.003   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00028 (    2)
  link_TRANS           : angle       0.47338 (    6)
  hydrogen bonds       : bond        0.04850 (  839)
  hydrogen bonds       : angle       3.19067 ( 2136)
  metal coordination   : bond        0.01163 (    8)
  metal coordination   : angle       5.48353 (    9)
  covalent geometry    : bond        0.00392 (15472)
  covalent geometry    : angle       0.56634 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8653 (tpt) cc_final: 0.8376 (tpp)
REVERT: G   23 LEU cc_start: 0.9231 (mt) cc_final: 0.8910 (mt)
REVERT: G   76 THR cc_start: 0.9176 (p) cc_final: 0.8823 (t)
REVERT: G   78 ILE cc_start: 0.9360 (mm) cc_final: 0.9092 (mm)
REVERT: G   95 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8723 (tttt)
REVERT: H   40 TYR cc_start: 0.8971 (m-80) cc_final: 0.8569 (m-10)
REVERT: H  120 LYS cc_start: 0.9312 (ttmt) cc_final: 0.8987 (tttp)
REVERT: K   79 ILE cc_start: 0.8047 (mm) cc_final: 0.7756 (mm)
REVERT: L    8 LYS cc_start: 0.9433 (tptp) cc_final: 0.9141 (tptm)
REVERT: L   26 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.7937 (m)
REVERT: L  101 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9288 (mmmm)
REVERT: L  139 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.8390 (mmt-90)
  outliers start: 28
  outliers final: 23
  residues processed: 206
  average time/residue: 0.3547
  time to fit residues: 99.3631
Evaluate side-chains
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 188
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0170
   chunk 47 optimal weight:    0.7980
   chunk 106 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 112 optimal weight:   20.0000
   chunk 45 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0970
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.138152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.085912 restraints weight = 41498.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.087057 restraints weight = 26207.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.087398 restraints weight = 20527.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15482  Z= 0.137
  Angle     :  0.551  10.572  22186  Z= 0.312
  Chirality :  0.034   0.169   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 28.892 177.884   4413
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.72 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.26), residues: 1057
  helix:  2.49 (0.20), residues: 652
  sheet:  0.80 (0.69), residues: 50
  loop : -0.64 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L  33 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.009   0.001   PHE K  53 
 TYR   0.014   0.001   TYR H  40 
 ARG   0.005   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00041 (    2)
  link_TRANS           : angle       0.28515 (    6)
  hydrogen bonds       : bond        0.04155 (  839)
  hydrogen bonds       : angle       2.97525 ( 2136)
  metal coordination   : bond        0.00994 (    8)
  metal coordination   : angle       4.91460 (    9)
  covalent geometry    : bond        0.00291 (15472)
  covalent geometry    : angle       0.54240 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8681 (m-10) cc_final: 0.8320 (m-10)
REVERT: F   84 MET cc_start: 0.8660 (mmm) cc_final: 0.8399 (mmm)
REVERT: G   23 LEU cc_start: 0.9146 (mt) cc_final: 0.8799 (mt)
REVERT: G   76 THR cc_start: 0.9133 (p) cc_final: 0.8867 (t)
REVERT: G   78 ILE cc_start: 0.9316 (mm) cc_final: 0.9033 (mm)
REVERT: G   95 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8728 (tttt)
REVERT: H   40 TYR cc_start: 0.8854 (m-80) cc_final: 0.8416 (m-10)
REVERT: H  120 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8981 (tttp)
REVERT: K   56 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8137 (tpp80)
REVERT: L    5 ARG cc_start: 0.8651 (tpt-90) cc_final: 0.8445 (tpt-90)
REVERT: L    8 LYS cc_start: 0.9413 (tptp) cc_final: 0.9045 (tptm)
REVERT: L   33 TRP cc_start: 0.8663 (m100) cc_final: 0.8426 (m100)
  outliers start: 21
  outliers final: 14
  residues processed: 212
  average time/residue: 0.3247
  time to fit residues: 93.2222
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 194
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0870
   chunk 124 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.1762

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
** M   2 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 = 0.3703 r_free = 0.3703 target = 0.135527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.081234 restraints weight = 42934.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.083293 restraints weight = 27347.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.084045 restraints weight = 18906.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  15482  Z= 0.190
  Angle     :  0.596  12.403  22186  Z= 0.333
  Chirality :  0.036   0.360   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 29.050 177.202   4413
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.80 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.26), residues: 1057
  helix:  2.35 (0.20), residues: 651
  sheet:  0.93 (0.68), residues: 50
  loop : -0.77 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 141 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.013   0.001   PHE H  70 
 TYR   0.025   0.002   TYR K  84 
 ARG   0.005   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00053 (    2)
  link_TRANS           : angle       0.43988 (    6)
  hydrogen bonds       : bond        0.04890 (  839)
  hydrogen bonds       : angle       3.20223 ( 2136)
  metal coordination   : bond        0.01065 (    8)
  metal coordination   : angle       5.34455 (    9)
  covalent geometry    : bond        0.00440 (15472)
  covalent geometry    : angle       0.58629 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8892 (m-10) cc_final: 0.8201 (m-10)
REVERT: D   83 TYR cc_start: 0.7523 (m-80) cc_final: 0.6484 (m-80)
REVERT: G   23 LEU cc_start: 0.9184 (mt) cc_final: 0.8855 (mt)
REVERT: G   76 THR cc_start: 0.9163 (p) cc_final: 0.8834 (t)
REVERT: G   78 ILE cc_start: 0.9388 (mm) cc_final: 0.9101 (mm)
REVERT: G   95 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8554 (ttpp)
REVERT: H   40 TYR cc_start: 0.8920 (m-80) cc_final: 0.8544 (m-10)
REVERT: H  120 LYS cc_start: 0.9286 (ttmt) cc_final: 0.9007 (tttp)
REVERT: K   56 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8242 (tpp80)
REVERT: L    8 LYS cc_start: 0.9435 (tptp) cc_final: 0.9085 (tptm)
REVERT: L   33 TRP cc_start: 0.8726 (m100) cc_final: 0.8341 (m100)
REVERT: L   78 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8477 (tp)
  outliers start: 27
  outliers final: 22
  residues processed: 207
  average time/residue: 0.3279
  time to fit residues: 92.0142
Evaluate side-chains
  212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 188
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 123 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 128 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    0.1980
   chunk 118 optimal weight:    0.8980
   chunk 111 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
L  32 HIS
** M   2 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 = 0.3697 r_free = 0.3697 target = 0.135092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.081527 restraints weight = 45741.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.083823 restraints weight = 27467.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.083958 restraints weight = 17520.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15482  Z= 0.193
  Angle     :  0.600  13.187  22186  Z= 0.333
  Chirality :  0.036   0.394   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 29.099 177.410   4413
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.91 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.26), residues: 1057
  helix:  2.25 (0.20), residues: 651
  sheet:  0.93 (0.69), residues: 50
  loop : -0.80 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP L 141 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.012   0.001   PHE H  70 
 TYR   0.022   0.002   TYR K  84 
 ARG   0.004   0.000   ARG D  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00069 (    2)
  link_TRANS           : angle       0.42968 (    6)
  hydrogen bonds       : bond        0.04912 (  839)
  hydrogen bonds       : angle       3.27070 ( 2136)
  metal coordination   : bond        0.01001 (    8)
  metal coordination   : angle       5.24304 (    9)
  covalent geometry    : bond        0.00446 (15472)
  covalent geometry    : angle       0.59100 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   23 LEU cc_start: 0.9190 (mt) cc_final: 0.8855 (mt)
REVERT: G   76 THR cc_start: 0.9172 (p) cc_final: 0.8843 (t)
REVERT: G   78 ILE cc_start: 0.9396 (mm) cc_final: 0.9108 (mm)
REVERT: G   95 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8556 (ttpp)
REVERT: H   40 TYR cc_start: 0.8937 (m-80) cc_final: 0.8590 (m-10)
REVERT: H  120 LYS cc_start: 0.9290 (ttmt) cc_final: 0.9032 (tttp)
REVERT: K   56 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8242 (tpp80)
REVERT: L    8 LYS cc_start: 0.9400 (tptp) cc_final: 0.9025 (tptm)
REVERT: L   33 TRP cc_start: 0.8674 (m100) cc_final: 0.8369 (m100)
REVERT: L   78 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8554 (tp)
  outliers start: 26
  outliers final: 20
  residues processed: 207
  average time/residue: 0.3364
  time to fit residues: 94.1784
Evaluate side-chains
  207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 17 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 126 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 115 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.136112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.082379 restraints weight = 44297.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.084397 restraints weight = 27091.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.084820 restraints weight = 18518.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15482  Z= 0.157
  Angle     :  0.598  13.874  22186  Z= 0.330
  Chirality :  0.036   0.455   2516
  Planarity :  0.004   0.047   1794
  Dihedral  : 29.058 177.721   4413
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.53 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.26), residues: 1057
  helix:  2.34 (0.21), residues: 653
  sheet:  0.82 (0.67), residues: 50
  loop : -0.78 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 141 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.010   0.001   PHE L  62 
 TYR   0.023   0.002   TYR K  84 
 ARG   0.004   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00019 (    2)
  link_TRANS           : angle       0.30601 (    6)
  hydrogen bonds       : bond        0.04577 (  839)
  hydrogen bonds       : angle       3.22788 ( 2136)
  metal coordination   : bond        0.00863 (    8)
  metal coordination   : angle       5.08756 (    9)
  covalent geometry    : bond        0.00353 (15472)
  covalent geometry    : angle       0.58905 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8931 (tpp) cc_final: 0.8604 (tpt)
REVERT: G   23 LEU cc_start: 0.9178 (mt) cc_final: 0.8833 (mt)
REVERT: G   76 THR cc_start: 0.9150 (p) cc_final: 0.8824 (t)
REVERT: G   78 ILE cc_start: 0.9374 (mm) cc_final: 0.9084 (mm)
REVERT: G   95 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (tttt)
REVERT: H   40 TYR cc_start: 0.8879 (m-80) cc_final: 0.8511 (m-10)
REVERT: H  120 LYS cc_start: 0.9276 (ttmt) cc_final: 0.9016 (tttp)
REVERT: K   56 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8216 (tpp80)
REVERT: L   33 TRP cc_start: 0.8721 (m100) cc_final: 0.8337 (m100)
REVERT: L   78 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8545 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 202
  average time/residue: 0.3350
  time to fit residues: 92.1429
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 73 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.096752 restraints weight = 34260.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.094915 restraints weight = 54580.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.096177 restraints weight = 43403.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  15482  Z= 0.200
  Angle     :  0.627  14.373  22186  Z= 0.344
  Chirality :  0.037   0.435   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 29.149 177.443   4413
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.42 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1057
  helix:  2.24 (0.21), residues: 651
  sheet:  0.67 (0.65), residues: 50
  loop : -0.86 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  77 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.013   0.001   PHE H  70 
 TYR   0.022   0.002   TYR K  84 
 ARG   0.006   0.000   ARG L  15 

Details of bonding type rmsd
  link_TRANS           : bond        0.00072 (    2)
  link_TRANS           : angle       0.43703 (    6)
  hydrogen bonds       : bond        0.05031 (  839)
  hydrogen bonds       : angle       3.35144 ( 2136)
  metal coordination   : bond        0.01001 (    8)
  metal coordination   : angle       5.30460 (    9)
  covalent geometry    : bond        0.00465 (15472)
  covalent geometry    : angle       0.61807 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8591 (m-10) cc_final: 0.7818 (m-10)
REVERT: D   57 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8414 (mppt)
REVERT: G   23 LEU cc_start: 0.9237 (mt) cc_final: 0.8966 (mt)
REVERT: G   76 THR cc_start: 0.9188 (p) cc_final: 0.8843 (t)
REVERT: G   78 ILE cc_start: 0.9384 (mm) cc_final: 0.9098 (mm)
REVERT: G   95 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8571 (ttpp)
REVERT: H   40 TYR cc_start: 0.8937 (m-80) cc_final: 0.8657 (m-10)
REVERT: L   78 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8387 (tp)
  outliers start: 24
  outliers final: 21
  residues processed: 202
  average time/residue: 0.3395
  time to fit residues: 92.5978
Evaluate side-chains
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0000
   chunk 115 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 120 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0170
   chunk 62 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4022

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  92 GLN
** M   2 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 = 0.3724 r_free = 0.3724 target = 0.137181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.097922 restraints weight = 33607.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.099689 restraints weight = 54279.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.100420 restraints weight = 34030.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15482  Z= 0.142
  Angle     :  0.598  15.483  22186  Z= 0.330
  Chirality :  0.035   0.463   2516
  Planarity :  0.004   0.043   1794
  Dihedral  : 29.004 178.013   4413
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.29 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.26), residues: 1057
  helix:  2.38 (0.21), residues: 652
  sheet:  0.51 (0.65), residues: 50
  loop : -0.76 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP L  33 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE L  56 
 TYR   0.024   0.002   TYR L 127 
 ARG   0.014   0.000   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00050 (    2)
  link_TRANS           : angle       0.18135 (    6)
  hydrogen bonds       : bond        0.04312 (  839)
  hydrogen bonds       : angle       3.18299 ( 2136)
  metal coordination   : bond        0.00806 (    8)
  metal coordination   : angle       4.82946 (    9)
  covalent geometry    : bond        0.00308 (15472)
  covalent geometry    : angle       0.59067 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8445 (m-10) cc_final: 0.7783 (m-10)
REVERT: G   23 LEU cc_start: 0.9213 (mt) cc_final: 0.8924 (mt)
REVERT: G   76 THR cc_start: 0.9147 (p) cc_final: 0.8890 (t)
REVERT: G   78 ILE cc_start: 0.9354 (mm) cc_final: 0.9069 (mm)
REVERT: G   95 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8732 (tttt)
REVERT: H   40 TYR cc_start: 0.8884 (m-80) cc_final: 0.8553 (m-10)
REVERT: K   56 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8142 (tpp80)
REVERT: L   78 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8369 (tp)
REVERT: L  135 ASN cc_start: 0.7964 (m-40) cc_final: 0.7705 (m-40)
  outliers start: 22
  outliers final: 18
  residues processed: 201
  average time/residue: 0.3263
  time to fit residues: 89.6457
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 111 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.133405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.079463 restraints weight = 53143.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.081623 restraints weight = 29754.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.081270 restraints weight = 22618.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    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 = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  15482  Z= 0.239
  Angle     :  0.654  14.969  22186  Z= 0.360
  Chirality :  0.038   0.440   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 29.222 177.302   4413
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.61 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.26), residues: 1057
  helix:  2.18 (0.21), residues: 652
  sheet:  0.40 (0.66), residues: 50
  loop : -0.91 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.004   TRP L  33 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.017   0.002   PHE H  70 
 TYR   0.021   0.002   TYR L 127 
 ARG   0.008   0.001   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00171 (    2)
  link_TRANS           : angle       0.50709 (    6)
  hydrogen bonds       : bond        0.05520 (  839)
  hydrogen bonds       : angle       3.48403 ( 2136)
  metal coordination   : bond        0.01140 (    8)
  metal coordination   : angle       5.56799 (    9)
  covalent geometry    : bond        0.00563 (15472)
  covalent geometry    : angle       0.64488 (22171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4828.60 seconds
wall clock time: 84 minutes 44.63 seconds (5084.63 seconds total)