Starting phenix.real_space_refine
on Thu Sep 18 16:33:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smx_40605/09_2025/8smx_40605.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smx_40605/09_2025/8smx_40605.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smx_40605/09_2025/8smx_40605.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smx_40605/09_2025/8smx_40605.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smx_40605/09_2025/8smx_40605.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smx_40605/09_2025/8smx_40605.cif"
  }
  resolution = 3.2
  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=   0.123
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 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: "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      32.756  69.086  46.490  1.00 27.36           S
  ATOM  12446  SG  CYS K  51      31.674  65.517  46.031  1.00 24.79           S
  ATOM  12470  SG  CYS K  54      32.868  67.529  43.025  1.00 27.29           S
  ATOM  12187  SG  CYS K  16      23.703  62.014  53.077  1.00 58.61           S
  ATOM  12205  SG  CYS K  19      21.687  59.882  55.391  1.00 62.50           S
  ATOM  12335  SG  CYS K  36      23.658  62.811  56.830  1.00 42.90           S
  ATOM  12357  SG  CYS K  39      25.492  59.705  55.463  1.00 39.01           S

  Time building chain proxies: 3.19, per 1000 atoms: 0.23
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 130.144, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2608      7.00
     C    7891      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: 1.03
  Conformation dependent library (CDL) restraints added in 344.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
      Number of angles added : 9


  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      64.1% alpha, 4.5% beta
      136 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.611A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.565A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.844A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.593A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.740A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.508A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.640A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.764A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.538A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 123
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.761A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.579A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.588A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    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 41
      removed outlier: 3.585A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.819A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.684A  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 26 through 37
      removed outlier: 3.559A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    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: 3.641A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.574A  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 37 through 46
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 3.858A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 74 through 84
      removed outlier: 4.158A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR K  84 " --> pdb=" O   ILE K  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.917A  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: 3.538A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.860A  pdb=" N   LEU L 110 " --> pdb=" O   ILE L 106 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASP L 111 " --> pdb=" O   ALA L 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 130 through 143
      removed outlier: 3.639A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.155A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.444A  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: 6.800A  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: 7.010A  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: 7.606A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25

    462 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2974
        1.33 -     1.45: 4495
        1.45 -     1.57: 6762
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.60e+00
  bond pdb=" CG  PRO L  61 "
       pdb=" CD  PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.512  1.478  0.034 2.70e-02 1.37e+03 1.57e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.39e+00
  bond pdb=" CB  ARG A 129 "
       pdb=" CG  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.01e+00
  bond pdb=" CB  THR K  66 "
       pdb=" CG2 THR K  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.17e-01
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 20929
        1.77 -     3.54: 395
        3.54 -     5.31: 22
        5.31 -     7.08: 5
        7.08 -     8.85: 2
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  121.55   -8.85 3.00e+00 1.11e-01 8.71e+00
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.56   -3.96 1.50e+00 4.44e-01 6.98e+00
  angle pdb=" C   LEU L  89 "
        pdb=" N   ARG L  90 "
        pdb=" CA  ARG L  90 "
      ideal   model   delta    sigma   weight residual
     122.58  117.16    5.42 2.07e+00 2.33e-01 6.85e+00
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.96   -5.78 2.37e+00 1.78e-01 5.94e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.62   -5.44 2.37e+00 1.78e-01 5.26e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.13: 6796
       35.13 -    70.26: 1411
       70.26 -   105.39: 21
      105.39 -   140.51: 0
      140.51 -   175.64: 2
  Dihedral angle restraints: 8230
    sinusoidal: 5306
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.36  175.64     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   66.14  153.86     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CA  PHE E  84 "
           pdb=" C   PHE E  84 "
           pdb=" N   GLN E  85 "
           pdb=" CA  GLN E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.10   16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1636
       0.030 -    0.061: 556
       0.061 -    0.091: 160
       0.091 -    0.121: 60
       0.121 -    0.151: 7
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CG  LEU L 103 "
            pdb=" CB  LEU L 103 "
            pdb=" CD1 LEU L 103 "
            pdb=" CD2 LEU L 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.73e-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    2.36    0.15 2.00e-01 2.50e+01 5.56e-01
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.026 2.00e-02 2.50e+03   1.14e-02 3.60e+00
        pdb=" N9   DA I -35 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.003 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 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.024 2.00e-02 2.50e+03   1.03e-02 3.20e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  17 "    0.024 2.00e-02 2.50e+03   1.06e-02 3.07e+00
        pdb=" N9   DA I  17 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8   DA I  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  17 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  17 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  17 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2062
        2.77 -     3.30: 11830
        3.30 -     3.83: 25259
        3.83 -     4.37: 31139
        4.37 -     4.90: 45796
  Nonbonded interactions: 116086
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.236 2.496
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" NZ  LYS D 116 "
            pdb=" O   ALA K  47 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.294 2.560
  ... (remaining 116081 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 individual isotropic
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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.610
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.147
  Angle     :  0.567   8.854  21368  Z= 0.333
  Chirality :  0.036   0.151   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 26.376 175.642   6336
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.43 (0.27), residues: 983
  helix:  1.97 (0.21), residues: 628
  sheet: -0.51 (0.92), residues: 24
  loop : -0.96 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  45 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  77 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (14864)
  covalent geometry    : angle       0.56577 (21353)
  hydrogen bonds       : bond        0.11293 (  811)
  hydrogen bonds       : angle       3.76124 ( 2062)
  metal coordination   : bond        0.00466 (    8)
  metal coordination   : angle       1.84038 (    9)
  link_TRANS           : bond        0.00193 (    2)
  link_TRANS           : angle       0.44603 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.394 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7865 (pttm) cc_final: 0.7286 (ptpp)
REVERT: D   35 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: D  116 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7592 (mtmm)
REVERT: E   53 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8015 (ttm170)
REVERT: H   54 ILE cc_start: 0.9102 (tt) cc_final: 0.8879 (tt)
REVERT: H  112 SER cc_start: 0.9103 (t) cc_final: 0.8481 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1763
  time to fit residues: 23.2612
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.1980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    3.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.170036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.127101 restraints weight = 27635.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.82
r_work: 0.2732 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    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 = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.0698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14874  Z= 0.147
  Angle     :  0.538   6.480  21368  Z= 0.319
  Chirality :  0.034   0.139   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.082 176.705   4332
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.44 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.75 (0.27), residues: 983
  helix:  2.23 (0.21), residues: 635
  sheet: -0.73 (0.91), residues: 24
  loop : -0.90 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  99 
 TYR   0.014   0.001   TYR G  50 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  77 
 HIS   0.003   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (14864)
  covalent geometry    : angle       0.53740 (21353)
  hydrogen bonds       : bond        0.04775 (  811)
  hydrogen bonds       : angle       2.88092 ( 2062)
  metal coordination   : bond        0.00418 (    8)
  metal coordination   : angle       1.72272 (    9)
  link_TRANS           : bond        0.00255 (    2)
  link_TRANS           : angle       0.30879 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8023 (mt-10)
REVERT: C  118 LYS cc_start: 0.7782 (pttm) cc_final: 0.7012 (ptpp)
REVERT: D   35 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8061 (mt-10)
REVERT: H   54 ILE cc_start: 0.9277 (tt) cc_final: 0.9043 (tt)
REVERT: H  112 SER cc_start: 0.9156 (t) cc_final: 0.8516 (m)
REVERT: K   60 SER cc_start: 0.8566 (t) cc_final: 0.8273 (m)
REVERT: L   78 ILE cc_start: 0.6138 (mp) cc_final: 0.5681 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1669
  time to fit residues: 22.5458
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 110 optimal weight:   30.0000
   overall best weight:    1.4786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.158658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.116422 restraints weight = 23951.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.98
r_work: 0.2626 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.0705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14874  Z= 0.212
  Angle     :  0.582   7.252  21368  Z= 0.340
  Chirality :  0.038   0.152   2419
  Planarity :  0.005   0.039   1688
  Dihedral  : 29.345 177.263   4332
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  6.07 %
    Favored  : 93.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.48 (0.26), residues: 983
  helix:  2.01 (0.21), residues: 638
  sheet: -0.60 (0.91), residues: 24
  loop : -1.04 (0.31), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  35 
 TYR   0.015   0.002   TYR G  50 
 PHE   0.012   0.002   PHE D  65 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (14864)
  covalent geometry    : angle       0.58067 (21353)
  hydrogen bonds       : bond        0.05868 (  811)
  hydrogen bonds       : angle       2.99825 ( 2062)
  metal coordination   : bond        0.00542 (    8)
  metal coordination   : angle       1.82247 (    9)
  link_TRANS           : bond        0.00048 (    2)
  link_TRANS           : angle       0.59732 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.444 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8155 (mt-10)
REVERT: C  118 LYS cc_start: 0.7892 (pttm) cc_final: 0.7097 (ptpp)
REVERT: D   35 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7957 (mt-10)
REVERT: H   54 ILE cc_start: 0.9288 (tt) cc_final: 0.9027 (tt)
REVERT: H  112 SER cc_start: 0.9181 (t) cc_final: 0.8554 (m)
REVERT: K   60 SER cc_start: 0.8628 (t) cc_final: 0.8356 (m)
REVERT: L   78 ILE cc_start: 0.6022 (mp) cc_final: 0.5628 (tp)
  outliers start: 3
  outliers final: 3
  residues processed: 101
  average time/residue: 0.1793
  time to fit residues: 24.1556
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   chunk 27 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 119 optimal weight:   40.0000
   chunk 106 optimal weight:    0.0980
   chunk 112 optimal weight:    8.9990
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.153069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.116774 restraints weight = 21010.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.95
r_work: 0.2766 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.0710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14874  Z= 0.209
  Angle     :  0.579   7.186  21368  Z= 0.338
  Chirality :  0.037   0.149   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.352 177.348   4332
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  7.24 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.43 (0.26), residues: 983
  helix:  1.99 (0.20), residues: 638
  sheet: -0.64 (0.91), residues: 24
  loop : -1.11 (0.30), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  35 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.012   0.002   PHE D  65 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (14864)
  covalent geometry    : angle       0.57733 (21353)
  hydrogen bonds       : bond        0.05801 (  811)
  hydrogen bonds       : angle       2.98090 ( 2062)
  metal coordination   : bond        0.00536 (    8)
  metal coordination   : angle       2.03105 (    9)
  link_TRANS           : bond        0.00155 (    2)
  link_TRANS           : angle       0.54279 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.388 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7925 (mt-10)
REVERT: C  118 LYS cc_start: 0.7892 (pttm) cc_final: 0.7074 (ptpp)
REVERT: D   35 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: H   54 ILE cc_start: 0.9266 (tt) cc_final: 0.9027 (tt)
REVERT: H  112 SER cc_start: 0.9130 (t) cc_final: 0.8465 (m)
REVERT: K   60 SER cc_start: 0.8545 (t) cc_final: 0.8273 (m)
REVERT: L   78 ILE cc_start: 0.6050 (mp) cc_final: 0.5648 (tp)
  outliers start: 4
  outliers final: 3
  residues processed: 98
  average time/residue: 0.1801
  time to fit residues: 23.4291
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain K residue   35 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0050
   chunk 113 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.6196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.157893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.122808 restraints weight = 28275.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.27
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.0702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14874  Z= 0.148
  Angle     :  0.556   7.297  21368  Z= 0.328
  Chirality :  0.035   0.138   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.327 176.898   4332
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.29 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.63 (0.26), residues: 983
  helix:  2.17 (0.21), residues: 636
  sheet: -0.75 (0.91), residues: 24
  loop : -1.04 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  35 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.009   0.001   PHE F  61 
 TRP   0.004   0.001   TRP K  77 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (14864)
  covalent geometry    : angle       0.55473 (21353)
  hydrogen bonds       : bond        0.05266 (  811)
  hydrogen bonds       : angle       2.98151 ( 2062)
  metal coordination   : bond        0.00473 (    8)
  metal coordination   : angle       1.82635 (    9)
  link_TRANS           : bond        0.00142 (    2)
  link_TRANS           : angle       0.59619 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.397 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7884 (pttm) cc_final: 0.7246 (ptpp)
REVERT: D   35 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7854 (mt-10)
REVERT: H   54 ILE cc_start: 0.9104 (tt) cc_final: 0.8870 (tt)
REVERT: H  112 SER cc_start: 0.9056 (t) cc_final: 0.8445 (m)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1903
  time to fit residues: 24.6061
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain K residue   35 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.159676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.116830 restraints weight = 21560.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.49
r_work: 0.2697 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14874  Z= 0.192
  Angle     :  0.562   7.167  21368  Z= 0.330
  Chirality :  0.037   0.144   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.337 177.221   4332
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.88 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.54 (0.26), residues: 983
  helix:  2.14 (0.20), residues: 636
  sheet: -0.75 (0.91), residues: 24
  loop : -1.17 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  35 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.011   0.002   PHE F  61 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (14864)
  covalent geometry    : angle       0.56070 (21353)
  hydrogen bonds       : bond        0.05518 (  811)
  hydrogen bonds       : angle       2.93799 ( 2062)
  metal coordination   : bond        0.00478 (    8)
  metal coordination   : angle       1.94898 (    9)
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.48171 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.367 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8052 (mt-10)
REVERT: C  118 LYS cc_start: 0.7878 (pttm) cc_final: 0.7103 (ptpp)
REVERT: D   35 GLU cc_start: 0.8207 (mt-10) cc_final: 0.8007 (mt-10)
REVERT: H   54 ILE cc_start: 0.9246 (tt) cc_final: 0.8992 (tt)
REVERT: H  112 SER cc_start: 0.9169 (t) cc_final: 0.8526 (m)
  outliers start: 6
  outliers final: 4
  residues processed: 99
  average time/residue: 0.1756
  time to fit residues: 23.2658
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.159952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.116595 restraints weight = 21072.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.41
r_work: 0.2705 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14874  Z= 0.179
  Angle     :  0.561   7.420  21368  Z= 0.329
  Chirality :  0.036   0.142   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.337 177.188   4332
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.58 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.57 (0.26), residues: 983
  helix:  2.17 (0.20), residues: 636
  sheet: -0.71 (0.92), residues: 24
  loop : -1.18 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  35 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.010   0.002   PHE F  61 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (14864)
  covalent geometry    : angle       0.56020 (21353)
  hydrogen bonds       : bond        0.05396 (  811)
  hydrogen bonds       : angle       2.92955 ( 2062)
  metal coordination   : bond        0.00475 (    8)
  metal coordination   : angle       1.89744 (    9)
  link_TRANS           : bond        0.00098 (    2)
  link_TRANS           : angle       0.59367 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.240 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7883 (pttm) cc_final: 0.7102 (ptpp)
REVERT: D   35 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: H   54 ILE cc_start: 0.9239 (tt) cc_final: 0.8990 (tt)
REVERT: H  112 SER cc_start: 0.9169 (t) cc_final: 0.8511 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 100
  average time/residue: 0.1639
  time to fit residues: 21.9795
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 107 optimal weight:    0.2980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.160282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.118478 restraints weight = 24911.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.17
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  14874  Z= 0.160
  Angle     :  0.554   7.134  21368  Z= 0.326
  Chirality :  0.035   0.139   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.331 177.118   4332
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.51 %
    Favored  : 88.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.63 (0.26), residues: 983
  helix:  2.22 (0.21), residues: 636
  sheet: -0.70 (0.92), residues: 24
  loop : -1.17 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 129 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.010   0.001   PHE F  61 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.008   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (14864)
  covalent geometry    : angle       0.55258 (21353)
  hydrogen bonds       : bond        0.05259 (  811)
  hydrogen bonds       : angle       2.92326 ( 2062)
  metal coordination   : bond        0.00447 (    8)
  metal coordination   : angle       1.86772 (    9)
  link_TRANS           : bond        0.00045 (    2)
  link_TRANS           : angle       0.59544 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.426 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7867 (pttm) cc_final: 0.7210 (ptpp)
REVERT: H   54 ILE cc_start: 0.9080 (tt) cc_final: 0.8818 (tt)
REVERT: H  112 SER cc_start: 0.9125 (t) cc_final: 0.8508 (m)
  outliers start: 6
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1735
  time to fit residues: 23.7095
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 116 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.163192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.120280 restraints weight = 28301.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.34
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14874  Z= 0.171
  Angle     :  0.554   7.279  21368  Z= 0.326
  Chirality :  0.036   0.138   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.327 177.154   4332
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.63 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.63 (0.26), residues: 983
  helix:  2.23 (0.20), residues: 635
  sheet: -0.70 (0.92), residues: 24
  loop : -1.18 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  32 
 TYR   0.008   0.001   TYR D 121 
 PHE   0.010   0.001   PHE F  61 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.006   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (14864)
  covalent geometry    : angle       0.55311 (21353)
  hydrogen bonds       : bond        0.05283 (  811)
  hydrogen bonds       : angle       2.91730 ( 2062)
  metal coordination   : bond        0.00455 (    8)
  metal coordination   : angle       1.85242 (    9)
  link_TRANS           : bond        0.00082 (    2)
  link_TRANS           : angle       0.58173 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.328 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7883 (pttm) cc_final: 0.7198 (ptpp)
REVERT: H   54 ILE cc_start: 0.9066 (tt) cc_final: 0.8801 (tt)
REVERT: H  112 SER cc_start: 0.9132 (t) cc_final: 0.8499 (m)
  outliers start: 6
  outliers final: 6
  residues processed: 100
  average time/residue: 0.1665
  time to fit residues: 22.4224
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain K residue   60 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 119 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 114 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.160308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.118727 restraints weight = 25484.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.18
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.0798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14874  Z= 0.162
  Angle     :  0.551   7.162  21368  Z= 0.325
  Chirality :  0.035   0.138   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.325 177.157   4332
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.75 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.26), residues: 983
  helix:  2.24 (0.21), residues: 635
  sheet: -0.69 (0.93), residues: 24
  loop : -1.17 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  35 
 TYR   0.008   0.001   TYR D 121 
 PHE   0.010   0.001   PHE F  61 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.008   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (14864)
  covalent geometry    : angle       0.54976 (21353)
  hydrogen bonds       : bond        0.05247 (  811)
  hydrogen bonds       : angle       2.91475 ( 2062)
  metal coordination   : bond        0.00439 (    8)
  metal coordination   : angle       1.85578 (    9)
  link_TRANS           : bond        0.00094 (    2)
  link_TRANS           : angle       0.59823 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.421 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7864 (pttm) cc_final: 0.7210 (ptpp)
REVERT: H   54 ILE cc_start: 0.9077 (tt) cc_final: 0.8814 (tt)
REVERT: H  112 SER cc_start: 0.9127 (t) cc_final: 0.8495 (m)
  outliers start: 7
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1856
  time to fit residues: 24.5098
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 109 optimal weight:    0.0020
   chunk 25 optimal weight:    0.0770
   chunk 30 optimal weight:    0.5980
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.3346

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.165576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.120497 restraints weight = 19525.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.27
r_work: 0.2754 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.0804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14874  Z= 0.142
  Angle     :  0.543   7.135  21368  Z= 0.322
  Chirality :  0.034   0.133   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.304 176.970   4332
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.63 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.27), residues: 983
  helix:  2.33 (0.21), residues: 635
  sheet: -0.67 (0.93), residues: 24
  loop : -1.11 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  68 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.009   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.008   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (14864)
  covalent geometry    : angle       0.54230 (21353)
  hydrogen bonds       : bond        0.04979 (  811)
  hydrogen bonds       : angle       2.90416 ( 2062)
  metal coordination   : bond        0.00415 (    8)
  metal coordination   : angle       1.78693 (    9)
  link_TRANS           : bond        0.00130 (    2)
  link_TRANS           : angle       0.59805 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2901.94 seconds
wall clock time: 50 minutes 16.80 seconds (3016.80 seconds total)