Starting phenix.real_space_refine
on Sat Oct 11 11:31:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn6_40614/10_2025/8sn6_40614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn6_40614/10_2025/8sn6_40614.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn6_40614/10_2025/8sn6_40614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn6_40614/10_2025/8sn6_40614.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn6_40614/10_2025/8sn6_40614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn6_40614/10_2025/8sn6_40614.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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      32.578  74.262  46.883  1.00 88.39           S
  ATOM  12446  SG  CYS K  51      31.271  71.186  45.070  1.00 91.68           S
  ATOM  12470  SG  CYS K  54      32.612  74.141  43.059  1.00 96.59           S
  ATOM  12187  SG  CYS K  16      22.251  68.673  52.194  1.00104.88           S
  ATOM  12205  SG  CYS K  19      20.908  65.621  54.027  1.00100.49           S
  ATOM  12335  SG  CYS K  36      23.441  67.769  55.828  1.00 94.61           S
  ATOM  12357  SG  CYS K  39      24.460  65.513  53.151  1.00 91.60           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.65, per 1000 atoms: 0.25
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (110.224, 134.128, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      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: 1.26
  Conformation dependent library (CDL) restraints added in 587.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      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:
      46 helices and 13 sheets defined
      62.9% alpha, 5.9% beta
      135 base pairs and 253 stacking pairs defined.
    Time for finding SS restraints: 1.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 3.587A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.560A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.873A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.846A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.504A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.564A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.672A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.539A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.824A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.600A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    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: 4.029A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.529A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.696A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.697A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.775A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.806A  pdb=" N   CYS K  14 " --> pdb=" O   SER K  10 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 10 through 15'
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 3.749A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.502A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE K  80 " --> pdb=" O   LEU K  76 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN K  81 " --> pdb=" O   TRP K  77 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.859A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.686A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.926A  pdb=" N   VAL L 102 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU L 103 " --> pdb=" O   ILE L  99 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.921A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 3.918A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.612A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.768A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 8.117A  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: 6.996A  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: 7.254A  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: 7.813A  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
      removed outlier: 3.805A  pdb=" N   VAL K  27 " --> pdb=" O   LEU K  35 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16

    496 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      253 stacking parallelities
  Total time for adding SS restraints: 2.78

  Time building geometry restraints manager: 1.70 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: 3591
        1.34 -     1.46: 4442
        1.46 -     1.58: 6804
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" CB  GLU K  25 "
       pdb=" CG  GLU K  25 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.90e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 9.68e-01
  bond pdb=" CB  MET D  59 "
       pdb=" CG  MET D  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.17e-01
  bond pdb=" C4'  DA I -35 "
       pdb=" C3'  DA I -35 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.019 2.00e-02 2.50e+03 8.82e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 21517
        1.47 -     2.94: 587
        2.94 -     4.41: 37
        4.41 -     5.88: 23
        5.88 -     7.35: 7
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.56   -6.02 1.91e+00 2.74e-01 9.94e+00
  angle pdb=" CA  ARG L 125 "
        pdb=" CB  ARG L 125 "
        pdb=" CG  ARG L 125 "
      ideal   model   delta    sigma   weight residual
     114.10  120.06   -5.96 2.00e+00 2.50e-01 8.88e+00
  angle pdb=" C   ASN L 135 "
        pdb=" N   ARG L 136 "
        pdb=" CA  ARG L 136 "
      ideal   model   delta    sigma   weight residual
     121.14  116.17    4.97 1.75e+00 3.27e-01 8.08e+00
  angle pdb=" CB  GLU K  25 "
        pdb=" CG  GLU K  25 "
        pdb=" CD  GLU K  25 "
      ideal   model   delta    sigma   weight residual
     112.60  117.37   -4.77 1.70e+00 3.46e-01 7.86e+00
  angle pdb=" C   PHE L  62 "
        pdb=" N   LYS L  63 "
        pdb=" CA  LYS L  63 "
      ideal   model   delta    sigma   weight residual
     122.74  129.55   -6.81 2.44e+00 1.68e-01 7.78e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.23: 7238
       35.23 -    70.47: 1347
       70.47 -   105.70: 24
      105.70 -   140.94: 0
      140.94 -   176.17: 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   36.17 -176.17     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   71.38  148.62     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CB  GLU G  56 "
           pdb=" CG  GLU G  56 "
           pdb=" CD  GLU G  56 "
           pdb=" OE1 GLU G  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.89   88.89     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1770
       0.032 -    0.064: 575
       0.064 -    0.096: 112
       0.096 -    0.128: 53
       0.128 -    0.160: 6
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  ARG L 125 "
            pdb=" N   ARG L 125 "
            pdb=" C   ARG L 125 "
            pdb=" CB  ARG L 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CA  LYS L 101 "
            pdb=" N   LYS L 101 "
            pdb=" C   LYS L 101 "
            pdb=" CB  LYS L 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU K  25 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   GLU K  25 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLU K  25 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PRO K  26 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.024 2.00e-02 2.50e+03   1.02e-02 2.84e+00
        pdb=" N9   DA I -35 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.000 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  33 "    0.009 2.00e-02 2.50e+03   1.02e-02 2.60e+00
        pdb=" CG  TRP L  33 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  33 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  33 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  33 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  33 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  33 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  33 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 233
        2.65 -     3.21: 12387
        3.21 -     3.77: 25809
        3.77 -     4.34: 32710
        4.34 -     4.90: 48516
  Nonbonded interactions: 119655
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.084 2.496
  nonbonded pdb=" O   ARG L 125 "
            pdb=" OG1 THR L 129 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   ASN G  73 "
            pdb=" ND2 ASN G  73 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.228 3.040
  ... (remaining 119650 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     17.530
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15482  Z= 0.169
  Angle     :  0.572   7.352  22186  Z= 0.327
  Chirality :  0.035   0.160   2516
  Planarity :  0.004   0.038   1794
  Dihedral  : 25.930 176.171   6577
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.26), residues: 1057
  helix:  2.41 (0.21), residues: 626
  sheet:  1.10 (0.75), residues: 50
  loop : -0.53 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  68 
 TYR   0.018   0.001   TYR H  83 
 PHE   0.015   0.001   PHE L  56 
 TRP   0.026   0.003   TRP L  33 
 HIS   0.002   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (15472)
  covalent geometry    : angle       0.56589 (22171)
  hydrogen bonds       : bond        0.10679 (  843)
  hydrogen bonds       : angle       4.14569 ( 2151)
  metal coordination   : bond        0.01060 (    8)
  metal coordination   : angle       4.15496 (    9)
  link_TRANS           : bond        0.00129 (    2)
  link_TRANS           : angle       0.51959 (    6)

*********************** 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
  243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.409 
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: A   81 ASP cc_start: 0.8084 (m-30) cc_final: 0.7869 (m-30)
REVERT: A   94 GLU cc_start: 0.8400 (tp30) cc_final: 0.7955 (mm-30)
REVERT: C   75 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8550 (mttm)
REVERT: C   95 LYS cc_start: 0.8850 (tptt) cc_final: 0.8643 (tptm)
REVERT: D   33 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7873 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8743 (mmt-90) cc_final: 0.8382 (mmt90)
REVERT: H  100 LEU cc_start: 0.9442 (mt) cc_final: 0.9172 (mp)
REVERT: K   42 SER cc_start: 0.7939 (p) cc_final: 0.7269 (p)
REVERT: K   66 THR cc_start: 0.7827 (m) cc_final: 0.7608 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1586
  time to fit residues: 52.3378
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.0050
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
M  41 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.131432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.082169 restraints weight = 46639.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.083364 restraints weight = 26506.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.083544 restraints weight = 20115.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.083698 restraints weight = 17902.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.083824 restraints weight = 17462.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.0983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.089  15482  Z= 0.158
  Angle     :  0.599  15.496  22186  Z= 0.333
  Chirality :  0.035   0.255   2516
  Planarity :  0.004   0.037   1794
  Dihedral  : 28.792 176.651   4413
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.85 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.26), residues: 1057
  helix:  2.44 (0.21), residues: 647
  sheet:  1.02 (0.71), residues: 55
  loop : -0.55 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  33 
 TYR   0.026   0.002   TYR L 134 
 PHE   0.031   0.002   PHE L  62 
 TRP   0.022   0.002   TRP L  33 
 HIS   0.005   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15472)
  covalent geometry    : angle       0.58360 (22171)
  hydrogen bonds       : bond        0.04565 (  843)
  hydrogen bonds       : angle       3.40155 ( 2151)
  metal coordination   : bond        0.03295 (    8)
  metal coordination   : angle       6.84245 (    9)
  link_TRANS           : bond        0.00237 (    2)
  link_TRANS           : angle       0.39467 (    6)

*********************** 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
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 209
  time to evaluate  : 0.440 
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: A   81 ASP cc_start: 0.8145 (m-30) cc_final: 0.7934 (m-30)
REVERT: A   94 GLU cc_start: 0.8341 (tp30) cc_final: 0.8086 (mm-30)
REVERT: C   95 LYS cc_start: 0.8912 (tptt) cc_final: 0.8633 (tptm)
REVERT: D   33 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.7805 (mtp-110)
REVERT: D   86 ARG cc_start: 0.8713 (mmt-90) cc_final: 0.8304 (mmt90)
REVERT: D  116 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8548 (ttpp)
REVERT: E  125 GLN cc_start: 0.8353 (mt0) cc_final: 0.8120 (mp10)
REVERT: K   66 THR cc_start: 0.8177 (m) cc_final: 0.7869 (m)
REVERT: K   68 ARG cc_start: 0.7575 (ptp90) cc_final: 0.6866 (mtm180)
REVERT: L   74 TYR cc_start: 0.8434 (t80) cc_final: 0.7791 (t80)
REVERT: L  110 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8742 (mm)
REVERT: L  134 TYR cc_start: 0.7706 (t80) cc_final: 0.6988 (t80)
REVERT: L  141 TRP cc_start: 0.8092 (t-100) cc_final: 0.7602 (t-100)
REVERT: M   42 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6976 (mmt180)
  outliers start: 12
  outliers final: 7
  residues processed: 215
  average time/residue: 0.1590
  time to fit residues: 46.8120
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 192
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   35 GLU
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  110 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 102 optimal weight:    0.4980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
L  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.130572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.085863 restraints weight = 41012.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.087565 restraints weight = 23701.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.087282 restraints weight = 21215.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.087837 restraints weight = 16255.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.088077 restraints weight = 14668.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  15482  Z= 0.161
  Angle     :  0.582  10.334  22186  Z= 0.325
  Chirality :  0.035   0.208   2516
  Planarity :  0.004   0.039   1794
  Dihedral  : 28.709 176.469   4413
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 1057
  helix:  2.47 (0.21), residues: 650
  sheet:  1.17 (0.73), residues: 50
  loop : -0.66 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  33 
 TYR   0.025   0.001   TYR H  83 
 PHE   0.018   0.001   PHE L  62 
 TRP   0.011   0.002   TRP L  33 
 HIS   0.004   0.001   HIS L   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (15472)
  covalent geometry    : angle       0.56939 (22171)
  hydrogen bonds       : bond        0.04430 (  843)
  hydrogen bonds       : angle       3.27773 ( 2151)
  metal coordination   : bond        0.02164 (    8)
  metal coordination   : angle       5.99488 (    9)
  link_TRANS           : bond        0.00110 (    2)
  link_TRANS           : angle       0.35375 (    6)

*********************** 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
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 201
  time to evaluate  : 0.418 
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: A   81 ASP cc_start: 0.8250 (m-30) cc_final: 0.8042 (m-30)
REVERT: A   94 GLU cc_start: 0.8289 (tp30) cc_final: 0.8036 (mm-30)
REVERT: C   95 LYS cc_start: 0.8939 (tptt) cc_final: 0.8628 (tptm)
REVERT: D   33 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7715 (mtp-110)
REVERT: E  125 GLN cc_start: 0.8487 (mt0) cc_final: 0.8071 (mp10)
REVERT: K   66 THR cc_start: 0.8369 (m) cc_final: 0.8053 (m)
REVERT: K   68 ARG cc_start: 0.7398 (ptp90) cc_final: 0.6848 (mtm180)
REVERT: L    8 LYS cc_start: 0.8693 (mppt) cc_final: 0.8331 (tptp)
REVERT: L  134 TYR cc_start: 0.6964 (t80) cc_final: 0.6547 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 207
  average time/residue: 0.1539
  time to fit residues: 43.6839
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 191
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 128 optimal weight:   20.0000
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
L  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.129461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.076258 restraints weight = 53538.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.078493 restraints weight = 27490.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.080043 restraints weight = 18608.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.080928 restraints weight = 15093.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.081273 restraints weight = 13575.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1362

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= 0.166
  Angle     :  0.584  11.042  22186  Z= 0.325
  Chirality :  0.035   0.163   2516
  Planarity :  0.004   0.046   1794
  Dihedral  : 28.702 176.428   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.42 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.26), residues: 1057
  helix:  2.45 (0.20), residues: 650
  sheet:  1.32 (0.75), residues: 50
  loop : -0.68 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  33 
 TYR   0.021   0.001   TYR H  83 
 PHE   0.015   0.001   PHE L  62 
 TRP   0.008   0.001   TRP L  93 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (15472)
  covalent geometry    : angle       0.57296 (22171)
  hydrogen bonds       : bond        0.04479 (  843)
  hydrogen bonds       : angle       3.21689 ( 2151)
  metal coordination   : bond        0.01920 (    8)
  metal coordination   : angle       5.61129 (    9)
  link_TRANS           : bond        0.00072 (    2)
  link_TRANS           : angle       0.33570 (    6)

*********************** 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
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8376 (tp30) cc_final: 0.8141 (mm-30)
REVERT: C   73 ASN cc_start: 0.8279 (t0) cc_final: 0.7994 (t0)
REVERT: C   95 LYS cc_start: 0.9021 (tptt) cc_final: 0.8669 (tptm)
REVERT: D   33 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7767 (mtp-110)
REVERT: E  125 GLN cc_start: 0.8474 (mt0) cc_final: 0.8214 (mt0)
REVERT: K   66 THR cc_start: 0.8396 (m) cc_final: 0.8070 (m)
REVERT: K   68 ARG cc_start: 0.7382 (ptp90) cc_final: 0.7132 (mtm180)
REVERT: L    4 LYS cc_start: 0.9370 (mptt) cc_final: 0.9149 (mptt)
REVERT: L    8 LYS cc_start: 0.8910 (mppt) cc_final: 0.8385 (tptp)
REVERT: L  134 TYR cc_start: 0.7903 (t80) cc_final: 0.7457 (t80)
REVERT: L  145 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.6080 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 208
  average time/residue: 0.1559
  time to fit residues: 44.2476
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 193
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 4 optimal weight:    0.0980
   chunk 78 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 126 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.129544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.077743 restraints weight = 45553.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.080792 restraints weight = 26838.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.080775 restraints weight = 18477.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.081436 restraints weight = 14972.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.081582 restraints weight = 14615.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15482  Z= 0.158
  Angle     :  0.583  12.043  22186  Z= 0.324
  Chirality :  0.035   0.299   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 28.695 176.584   4413
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.39 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.26), residues: 1057
  helix:  2.45 (0.20), residues: 650
  sheet:  1.49 (0.75), residues: 50
  loop : -0.64 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L  90 
 TYR   0.018   0.001   TYR H  83 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.010   0.002   TRP L  93 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (15472)
  covalent geometry    : angle       0.57356 (22171)
  hydrogen bonds       : bond        0.04355 (  843)
  hydrogen bonds       : angle       3.16929 ( 2151)
  metal coordination   : bond        0.01772 (    8)
  metal coordination   : angle       5.26971 (    9)
  link_TRANS           : bond        0.00072 (    2)
  link_TRANS           : angle       0.28224 (    6)

*********************** 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
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8270 (tp30) cc_final: 0.8010 (mm-30)
REVERT: C   73 ASN cc_start: 0.8324 (t0) cc_final: 0.8105 (t0)
REVERT: C   95 LYS cc_start: 0.9021 (tptt) cc_final: 0.8678 (tptm)
REVERT: D   33 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7754 (mtp-110)
REVERT: D  116 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8471 (ttpp)
REVERT: E  125 GLN cc_start: 0.8494 (mt0) cc_final: 0.8168 (mt0)
REVERT: K   66 THR cc_start: 0.8352 (m) cc_final: 0.8029 (m)
REVERT: K   68 ARG cc_start: 0.7528 (ptp90) cc_final: 0.7257 (mtm180)
REVERT: L    4 LYS cc_start: 0.9447 (mptt) cc_final: 0.9218 (mptt)
REVERT: L    8 LYS cc_start: 0.8972 (mppt) cc_final: 0.8427 (tptp)
REVERT: L   69 PHE cc_start: 0.7978 (m-80) cc_final: 0.7677 (m-80)
REVERT: L  134 TYR cc_start: 0.8180 (t80) cc_final: 0.7735 (t80)
REVERT: L  145 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6202 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 211
  average time/residue: 0.1633
  time to fit residues: 46.6868
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 198
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 9 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 122 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
M  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.130053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.090739 restraints weight = 45234.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.091210 restraints weight = 43569.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.091999 restraints weight = 37316.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.091977 restraints weight = 23993.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.093456 restraints weight = 20430.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15482  Z= 0.155
  Angle     :  0.593  13.643  22186  Z= 0.328
  Chirality :  0.035   0.310   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 28.691 176.601   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.26 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.26), residues: 1057
  helix:  2.45 (0.20), residues: 650
  sheet:  1.48 (0.74), residues: 49
  loop : -0.60 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.016   0.001   TYR H  83 
 PHE   0.013   0.001   PHE L  62 
 TRP   0.011   0.001   TRP L  93 
 HIS   0.003   0.001   HIS L   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (15472)
  covalent geometry    : angle       0.58459 (22171)
  hydrogen bonds       : bond        0.04293 (  843)
  hydrogen bonds       : angle       3.13683 ( 2151)
  metal coordination   : bond        0.01581 (    8)
  metal coordination   : angle       5.10867 (    9)
  link_TRANS           : bond        0.00075 (    2)
  link_TRANS           : angle       0.26602 (    6)

*********************** 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
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8093 (tp30) cc_final: 0.7791 (mm-30)
REVERT: C   16 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7933 (t)
REVERT: C   73 ASN cc_start: 0.8394 (t0) cc_final: 0.8100 (t0)
REVERT: C   95 LYS cc_start: 0.9025 (tptt) cc_final: 0.8640 (tptm)
REVERT: D   33 ARG cc_start: 0.8256 (mtp-110) cc_final: 0.7762 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8728 (pm20) cc_final: 0.8341 (pm20)
REVERT: E   94 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7688 (mm-30)
REVERT: E  125 GLN cc_start: 0.8518 (mt0) cc_final: 0.8139 (mt0)
REVERT: K   66 THR cc_start: 0.8380 (m) cc_final: 0.8054 (m)
REVERT: L    8 LYS cc_start: 0.8678 (mppt) cc_final: 0.8297 (tptp)
REVERT: L   69 PHE cc_start: 0.7547 (m-80) cc_final: 0.7253 (m-80)
REVERT: L  101 LYS cc_start: 0.8596 (pttp) cc_final: 0.8277 (pttp)
REVERT: L  145 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5905 (m-10)
REVERT: M   42 ARG cc_start: 0.6379 (mmt180) cc_final: 0.6041 (mmt180)
  outliers start: 17
  outliers final: 11
  residues processed: 215
  average time/residue: 0.1613
  time to fit residues: 47.3913
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 198
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** 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 = 0.3699 r_free = 0.3699 target = 0.129241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.078759 restraints weight = 46982.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.079767 restraints weight = 27275.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.080420 restraints weight = 20037.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.080617 restraints weight = 17621.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.080779 restraints weight = 16659.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15482  Z= 0.171
  Angle     :  0.613  14.415  22186  Z= 0.337
  Chirality :  0.036   0.276   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.737 176.353   4413
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.13 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.26), residues: 1057
  helix:  2.41 (0.21), residues: 650
  sheet:  1.46 (0.74), residues: 49
  loop : -0.63 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L  90 
 TYR   0.042   0.002   TYR L 134 
 PHE   0.010   0.001   PHE L  62 
 TRP   0.010   0.001   TRP L  93 
 HIS   0.003   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (15472)
  covalent geometry    : angle       0.60391 (22171)
  hydrogen bonds       : bond        0.04481 (  843)
  hydrogen bonds       : angle       3.20378 ( 2151)
  metal coordination   : bond        0.01697 (    8)
  metal coordination   : angle       5.16722 (    9)
  link_TRANS           : bond        0.00058 (    2)
  link_TRANS           : angle       0.31107 (    6)

*********************** 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: 15
    poor density    : 203
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9285 (t) cc_final: 0.8995 (t)
REVERT: A   94 GLU cc_start: 0.8263 (tp30) cc_final: 0.7968 (mm-30)
REVERT: C   73 ASN cc_start: 0.8325 (t0) cc_final: 0.8117 (t0)
REVERT: C   95 LYS cc_start: 0.9036 (tptt) cc_final: 0.8687 (tptm)
REVERT: D   33 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7767 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8703 (pm20) cc_final: 0.8309 (pm20)
REVERT: E  125 GLN cc_start: 0.8542 (mt0) cc_final: 0.8226 (mt0)
REVERT: H  119 THR cc_start: 0.9508 (t) cc_final: 0.9239 (t)
REVERT: K   66 THR cc_start: 0.8413 (m) cc_final: 0.8107 (m)
REVERT: L    8 LYS cc_start: 0.9000 (mppt) cc_final: 0.8536 (tptp)
REVERT: L   69 PHE cc_start: 0.8157 (m-80) cc_final: 0.7887 (m-80)
REVERT: L   74 TYR cc_start: 0.8348 (t80) cc_final: 0.7970 (t80)
REVERT: L   75 HIS cc_start: 0.8339 (t-90) cc_final: 0.7790 (t-90)
REVERT: L  134 TYR cc_start: 0.7998 (t80) cc_final: 0.7401 (t80)
REVERT: L  145 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6442 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 210
  average time/residue: 0.1581
  time to fit residues: 45.2858
Evaluate side-chains
  216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 202
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   chunk 127 optimal weight:   30.0000
   chunk 4 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0870
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.130229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.081206 restraints weight = 51400.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.081366 restraints weight = 28082.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.082167 restraints weight = 18843.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.082474 restraints weight = 17899.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.082548 restraints weight = 16066.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15482  Z= 0.149
  Angle     :  0.605  14.179  22186  Z= 0.331
  Chirality :  0.035   0.324   2516
  Planarity :  0.004   0.045   1794
  Dihedral  : 28.693 176.839   4413
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.34 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.26), residues: 1057
  helix:  2.45 (0.21), residues: 650
  sheet:  1.36 (0.75), residues: 49
  loop : -0.55 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG L  90 
 TYR   0.022   0.001   TYR L 134 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.013   0.002   TRP L  93 
 HIS   0.005   0.001   HIS L   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (15472)
  covalent geometry    : angle       0.59418 (22171)
  hydrogen bonds       : bond        0.04179 (  843)
  hydrogen bonds       : angle       3.11221 ( 2151)
  metal coordination   : bond        0.01603 (    8)
  metal coordination   : angle       5.66938 (    9)
  link_TRANS           : bond        0.00078 (    2)
  link_TRANS           : angle       0.23533 (    6)

*********************** 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
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9286 (t) cc_final: 0.9069 (t)
REVERT: A   94 GLU cc_start: 0.8155 (tp30) cc_final: 0.7863 (mm-30)
REVERT: C   16 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7958 (t)
REVERT: C   73 ASN cc_start: 0.8320 (t0) cc_final: 0.8059 (t0)
REVERT: C   95 LYS cc_start: 0.8988 (tptt) cc_final: 0.8646 (tptm)
REVERT: D   33 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7786 (mtp-110)
REVERT: E   59 GLU cc_start: 0.8754 (pm20) cc_final: 0.8376 (pm20)
REVERT: E   94 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7900 (mm-30)
REVERT: E  125 GLN cc_start: 0.8463 (mt0) cc_final: 0.8136 (mt0)
REVERT: H  119 THR cc_start: 0.9512 (t) cc_final: 0.9252 (t)
REVERT: L    8 LYS cc_start: 0.8957 (mppt) cc_final: 0.8519 (tptp)
REVERT: L    9 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8287 (mm-30)
REVERT: L   69 PHE cc_start: 0.8091 (m-80) cc_final: 0.7823 (m-80)
REVERT: L   74 TYR cc_start: 0.8516 (t80) cc_final: 0.8140 (t80)
REVERT: L   75 HIS cc_start: 0.8389 (t-90) cc_final: 0.7851 (t-90)
REVERT: L   93 TRP cc_start: 0.8428 (t-100) cc_final: 0.8126 (t-100)
REVERT: L  134 TYR cc_start: 0.7769 (t80) cc_final: 0.7270 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 218
  average time/residue: 0.1599
  time to fit residues: 47.7223
Evaluate side-chains
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 204
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   chunk 87 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.131513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.091538 restraints weight = 39880.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.092032 restraints weight = 38850.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.092280 restraints weight = 41732.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.093051 restraints weight = 24968.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.094115 restraints weight = 21326.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15482  Z= 0.142
  Angle     :  0.613  14.378  22186  Z= 0.332
  Chirality :  0.035   0.303   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.654 177.012   4413
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.42 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.26), residues: 1057
  helix:  2.47 (0.21), residues: 651
  sheet:  1.33 (0.75), residues: 49
  loop : -0.54 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG L  90 
 TYR   0.018   0.001   TYR L 134 
 PHE   0.025   0.001   PHE L  62 
 TRP   0.006   0.001   TRP L  93 
 HIS   0.003   0.000   HIS L   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (15472)
  covalent geometry    : angle       0.60602 (22171)
  hydrogen bonds       : bond        0.03957 (  843)
  hydrogen bonds       : angle       3.08048 ( 2151)
  metal coordination   : bond        0.01276 (    8)
  metal coordination   : angle       4.68227 (    9)
  link_TRANS           : bond        0.00086 (    2)
  link_TRANS           : angle       0.17787 (    6)

*********************** 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
  233 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 216
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9285 (t) cc_final: 0.8992 (t)
REVERT: A   94 GLU cc_start: 0.8064 (tp30) cc_final: 0.7820 (mm-30)
REVERT: C   16 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7812 (t)
REVERT: C   73 ASN cc_start: 0.8377 (t0) cc_final: 0.8082 (t0)
REVERT: C   95 LYS cc_start: 0.9004 (tptt) cc_final: 0.8636 (tptm)
REVERT: D   33 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7774 (mtp-110)
REVERT: D  116 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8563 (ttpp)
REVERT: E   94 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7818 (mm-30)
REVERT: E  125 GLN cc_start: 0.8407 (mt0) cc_final: 0.8002 (mt0)
REVERT: H  119 THR cc_start: 0.9510 (t) cc_final: 0.9251 (t)
REVERT: L   69 PHE cc_start: 0.7663 (m-80) cc_final: 0.7458 (m-80)
REVERT: L   75 HIS cc_start: 0.7838 (t-90) cc_final: 0.7331 (t-90)
REVERT: L  134 TYR cc_start: 0.6851 (t80) cc_final: 0.6641 (t80)
REVERT: L  143 GLN cc_start: 0.9139 (mm110) cc_final: 0.8893 (mp10)
  outliers start: 17
  outliers final: 11
  residues processed: 225
  average time/residue: 0.1549
  time to fit residues: 47.4762
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 207
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 111 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 121 optimal weight:    0.9980
   chunk 86 optimal weight:    6.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** 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 = 0.3692 r_free = 0.3692 target = 0.128739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.077756 restraints weight = 53926.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.079195 restraints weight = 30383.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.080208 restraints weight = 20340.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.080687 restraints weight = 17907.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.080448 restraints weight = 16383.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15482  Z= 0.195
  Angle     :  0.655  14.583  22186  Z= 0.353
  Chirality :  0.037   0.330   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.799 176.083   4413
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.53 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.26), residues: 1057
  helix:  2.34 (0.21), residues: 648
  sheet:  1.34 (0.79), residues: 43
  loop : -0.47 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  90 
 TYR   0.030   0.002   TYR L 134 
 PHE   0.015   0.002   PHE L  62 
 TRP   0.013   0.002   TRP L  93 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (15472)
  covalent geometry    : angle       0.64696 (22171)
  hydrogen bonds       : bond        0.04748 (  843)
  hydrogen bonds       : angle       3.28754 ( 2151)
  metal coordination   : bond        0.01696 (    8)
  metal coordination   : angle       5.03366 (    9)
  link_TRANS           : bond        0.00097 (    2)
  link_TRANS           : angle       0.32997 (    6)

********************** 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
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9336 (t) cc_final: 0.9110 (t)
REVERT: A   94 GLU cc_start: 0.8265 (tp30) cc_final: 0.8027 (mm-30)
REVERT: C   16 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7958 (t)
REVERT: C   73 ASN cc_start: 0.8413 (t0) cc_final: 0.8172 (t0)
REVERT: C   95 LYS cc_start: 0.9047 (tptt) cc_final: 0.8665 (tptm)
REVERT: D   33 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7782 (mtp-110)
REVERT: E   94 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7978 (mm-30)
REVERT: E  125 GLN cc_start: 0.8497 (mt0) cc_final: 0.8226 (mt0)
REVERT: H  119 THR cc_start: 0.9541 (t) cc_final: 0.9283 (t)
REVERT: L    9 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8432 (mm-30)
REVERT: L   69 PHE cc_start: 0.8216 (m-80) cc_final: 0.7951 (m-80)
REVERT: L   74 TYR cc_start: 0.8463 (t80) cc_final: 0.7786 (t80)
REVERT: L  134 TYR cc_start: 0.7835 (t80) cc_final: 0.7109 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 211
  average time/residue: 0.1625
  time to fit residues: 46.4799
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 197
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 113 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 123 optimal weight:   40.0000
   chunk 127 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.127026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.075804 restraints weight = 46610.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.077150 restraints weight = 27091.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.077192 restraints weight = 20173.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.077616 restraints weight = 18575.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.077739 restraints weight = 16662.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  15482  Z= 0.231
  Angle     :  0.686  14.318  22186  Z= 0.369
  Chirality :  0.038   0.305   2516
  Planarity :  0.005   0.043   1794
  Dihedral  : 28.917 175.526   4413
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.32 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.26), residues: 1057
  helix:  2.13 (0.21), residues: 648
  sheet:  1.41 (0.80), residues: 43
  loop : -0.57 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  90 
 TYR   0.022   0.002   TYR L 134 
 PHE   0.013   0.002   PHE K  40 
 TRP   0.035   0.003   TRP L  33 
 HIS   0.004   0.001   HIS L  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (15472)
  covalent geometry    : angle       0.67754 (22171)
  hydrogen bonds       : bond        0.05188 (  843)
  hydrogen bonds       : angle       3.44901 ( 2151)
  metal coordination   : bond        0.01903 (    8)
  metal coordination   : angle       5.41088 (    9)
  link_TRANS           : bond        0.00146 (    2)
  link_TRANS           : angle       0.48881 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2677.10 seconds
wall clock time: 46 minutes 45.36 seconds (2805.36 seconds total)