Starting phenix.real_space_refine
on Fri Sep 11 14:23:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t7a_10391/09_2026/6t7a_10391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t7a_10391/09_2026/6t7a_10391.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/6t7a_10391/09_2026/6t7a_10391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t7a_10391/09_2026/6t7a_10391.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t7a_10391/09_2026/6t7a_10391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t7a_10391/09_2026/6t7a_10391.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=   0.003 sd=   0.021
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: 5
    Type Number    sf(0)   Gaussians
     P     190      5.49       5
     S      10      5.16       5
     C    5889      2.51       5
     N    1960      2.21       5
     O    2289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10338
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 809
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 698
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 703
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1936
          Classifications: {'DNA': 95}
          Link IDs: {'rna3p': 94}
    Chain: "J"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1959
          Classifications: {'DNA': 95}
          Link IDs: {'rna3p': 94}
    Chain: "K"
      Number of atoms: 307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 307
          Classifications: {'peptide': 77}
          Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 71}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 374
          Unresolved non-hydrogen angles: 517
          Unresolved non-hydrogen dihedrals: 268
          Unresolved non-hydrogen chiralities: 86
          Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3}
          Unresolved non-hydrogen planarities: 178
  Time building chain proxies: 2.24, per 1000 atoms: 0.22
  Number of scatterers: 10338
  At special positions: 0
  Unit cell: (85.05, 115.5, 129.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     190     15.00
     O    2289      8.00
     N    1960      7.00
     C    5889      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 261.3 milliseconds
  

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 8 sheets defined
      68.2% alpha, 1.9% beta
      93 base pairs and 171 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.965A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.511A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.534A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
      removed outlier: 3.769A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 4.227A  pdb=" N   ARG B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.160A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.810A  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 45 through 73
      removed outlier: 4.184A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.552A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.540A  pdb=" N   VAL D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR D  39 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.585A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 4.331A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.722A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 31 through 41
      removed outlier: 4.046A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 47 through 49
      No H-bonds generated for 'chain 'F' and resid 47 through 49'
    Processing helix  chain 'F' and resid 50 through 76
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.809A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.185A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.552A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.540A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR H  39 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 53 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.584A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 4.331A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 54 through 71
      removed outlier: 3.602A  pdb=" N   VAL K  58 " --> pdb=" O   ASN K  54 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 75 through 90
    Processing helix  chain 'K' and resid 91 through 94
    Processing helix  chain 'K' and resid 95 through 113
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.875A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.264A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.451A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.507A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.375A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78

    408 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      216 hydrogen bonds
      432 hydrogen bond angles
      0 basepair planarities
      93 basepair parallelities
      171 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1653
        1.33 -     1.44: 3477
        1.44 -     1.56: 5364
        1.56 -     1.68: 378
        1.68 -     1.80: 20
  Bond restraints: 10892
  Sorted by residual:
  bond pdb=" C3'  DA J  89 "
       pdb=" O3'  DA J  89 "
    ideal  model  delta    sigma   weight residual
    1.435  1.384  0.051 1.30e-02 5.92e+03 1.51e+01
  bond pdb=" C3'  DT I  87 "
       pdb=" O3'  DT I  87 "
    ideal  model  delta    sigma   weight residual
    1.435  1.484 -0.049 1.30e-02 5.92e+03 1.44e+01
  bond pdb=" C3'  DG I  68 "
       pdb=" O3'  DG I  68 "
    ideal  model  delta    sigma   weight residual
    1.435  1.394  0.041 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" C3'  DA J 102 "
       pdb=" O3'  DA J 102 "
    ideal  model  delta    sigma   weight residual
    1.435  1.394  0.041 1.30e-02 5.92e+03 9.86e+00
  bond pdb=" C3'  DT J  38 "
       pdb=" C2'  DT J  38 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.70e+00
  ... (remaining 10887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 14291
        1.85 -     3.69: 1084
        3.69 -     5.54: 69
        5.54 -     7.39: 14
        7.39 -     9.23: 6
  Bond angle restraints: 15464
  Sorted by residual:
  angle pdb=" O4'  DT I  92 "
        pdb=" C4'  DT I  92 "
        pdb=" C3'  DT I  92 "
      ideal   model   delta    sigma   weight residual
     106.00  102.41    3.59 6.00e-01 2.78e+00 3.58e+01
  angle pdb=" N   ILE F  34 "
        pdb=" CA  ILE F  34 "
        pdb=" C   ILE F  34 "
      ideal   model   delta    sigma   weight residual
     112.96  107.02    5.94 1.00e+00 1.00e+00 3.53e+01
  angle pdb=" O4'  DA I  26 "
        pdb=" C4'  DA I  26 "
        pdb=" C3'  DA I  26 "
      ideal   model   delta    sigma   weight residual
     106.00  102.55    3.45 6.00e-01 2.78e+00 3.30e+01
  angle pdb=" C3'  DT I  87 "
        pdb=" O3'  DT I  87 "
        pdb=" P    DT I  88 "
      ideal   model   delta    sigma   weight residual
     119.70  126.06   -6.36 1.20e+00 6.94e-01 2.81e+01
  angle pdb=" C3'  DT I  88 "
        pdb=" C2'  DT I  88 "
        pdb=" C1'  DT I  88 "
      ideal   model   delta    sigma   weight residual
     102.50   96.29    6.21 1.20e+00 6.94e-01 2.68e+01
  ... (remaining 15459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.65: 4324
       19.65 -    39.31: 919
       39.31 -    58.96: 783
       58.96 -    78.61: 52
       78.61 -    98.26: 17
  Dihedral angle restraints: 6095
    sinusoidal: 3789
      harmonic: 2306
  Sorted by residual:
  dihedral pdb=" CA  LYS D  27 "
           pdb=" C   LYS D  27 "
           pdb=" N   ARG D  28 "
           pdb=" CA  ARG D  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.71   27.29     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  LYS H  27 "
           pdb=" C   LYS H  27 "
           pdb=" N   ARG H  28 "
           pdb=" CA  ARG H  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.78   27.22     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  ILE B  29 "
           pdb=" C   ILE B  29 "
           pdb=" N   THR B  30 "
           pdb=" CA  THR B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.79  -21.21     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 6092 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1148
       0.048 -    0.096: 440
       0.096 -    0.144: 110
       0.144 -    0.191: 15
       0.191 -    0.239: 2
  Chirality restraints: 1715
  Sorted by residual:
  chirality pdb=" CB  THR C  59 "
            pdb=" CA  THR C  59 "
            pdb=" OG1 THR C  59 "
            pdb=" CG2 THR C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  THR G  59 "
            pdb=" CA  THR G  59 "
            pdb=" OG1 THR G  59 "
            pdb=" CG2 THR G  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" C3'  DA J  55 "
            pdb=" C4'  DA J  55 "
            pdb=" O3'  DA J  55 "
            pdb=" C2'  DA J  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.47e-01
  ... (remaining 1712 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  24 "    0.020 2.00e-02 2.50e+03   3.97e-02 1.57e+01
        pdb=" C   ASP F  24 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   ASP F  24 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ASN F  25 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  60 "    0.028 2.00e-02 2.50e+03   1.50e-02 5.64e+00
        pdb=" N1   DT I  60 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2   DT I  60 "   -0.014 2.00e-02 2.50e+03
        pdb=" O2   DT I  60 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I  60 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DT I  60 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT I  60 "    0.013 2.00e-02 2.50e+03
        pdb=" C5   DT I  60 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I  60 "   -0.012 2.00e-02 2.50e+03
        pdb=" C6   DT I  60 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO C  80 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 146
        2.62 -     3.19: 7862
        3.19 -     3.76: 18565
        3.76 -     4.33: 24486
        4.33 -     4.90: 35606
  Nonbonded interactions: 86665
  Sorted by model distance:
  nonbonded pdb=" CB  GLU E  73 "
            pdb=" CG  ASN F  25 "
     model   vdw
     2.044 2.936
  nonbonded pdb=" CD  GLU E  73 "
            pdb=" CG  ASN F  25 "
     model   vdw
     2.167 2.800
  nonbonded pdb=" OE1 GLU E  73 "
            pdb=" CB  ASN F  25 "
     model   vdw
     2.167 3.440
  nonbonded pdb=" CB  HIS F  18 "
            pdb=" OP1  DT I  87 "
     model   vdw
     2.168 3.440
  nonbonded pdb=" CG  GLU E  73 "
            pdb=" OD1 ASN F  25 "
     model   vdw
     2.219 2.752
  ... (remaining 86660 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 16 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.010
  Find NCS groups from input model:        0.130
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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      :  0.010   0.697  10893  Z= 0.885
  Angle     :  0.984   9.233  15464  Z= 0.796
  Chirality :  0.053   0.239   1715
  Planarity :  0.006   0.058   1327
  Dihedral  : 26.125  98.264   4657
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.81 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.03 (0.23), residues: 829
  helix: -1.95 (0.16), residues: 569
  sheet:  None (None), residues: 0
  loop : -1.70 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  92 
 TYR   0.027   0.002   TYR F  98 
 PHE   0.009   0.002   PHE D  62 
 HIS   0.006   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00736 /  0.58 (10892)
  covalent geometry    : angle       0.98383 /  0.80 (15464)
  hydrogen bonds       : bond        0.11019 /  6.78 (  624)
  hydrogen bonds       : angle       4.77767 /  3.29 ( 1641)
  Misc. bond           : bond        0.69718 / 36.69 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 342
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TYR cc_start: 0.9019 (t80) cc_final: 0.8623 (t80)
REVERT: B   59 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8235 (mtpt)
REVERT: B   60 VAL cc_start: 0.9049 (m) cc_final: 0.8010 (p)
REVERT: B   63 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: B   92 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7676 (ttp80)
REVERT: C   73 ASN cc_start: 0.8815 (t0) cc_final: 0.8555 (t0)
REVERT: C   84 GLN cc_start: 0.8744 (tp40) cc_final: 0.8353 (tp-100)
REVERT: D   85 THR cc_start: 0.9519 (m) cc_final: 0.9107 (p)
REVERT: E   86 SER cc_start: 0.8750 (m) cc_final: 0.8499 (m)
REVERT: E  124 ILE cc_start: 0.9285 (mt) cc_final: 0.8917 (mp)
REVERT: F   59 LYS cc_start: 0.8804 (tttm) cc_final: 0.8598 (tttm)
REVERT: F   60 VAL cc_start: 0.9172 (p) cc_final: 0.8677 (m)
REVERT: F   70 VAL cc_start: 0.9486 (t) cc_final: 0.8584 (t)
REVERT: F   71 THR cc_start: 0.9269 (p) cc_final: 0.8684 (p)
REVERT: G   56 GLU cc_start: 0.8181 (tt0) cc_final: 0.7931 (tt0)
REVERT: G   71 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8617 (ttp80)
REVERT: H   51 ILE cc_start: 0.8660 (tt) cc_final: 0.8418 (tt)
REVERT: H   73 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7633 (mm-30)
REVERT: H   80 TYR cc_start: 0.8678 (m-10) cc_final: 0.7978 (m-10)
REVERT: H   85 THR cc_start: 0.9140 (m) cc_final: 0.8627 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 342
  average time/residue: 0.1549
  time to fit residues: 66.7429
Evaluate side-chains
  232 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.3980
   chunk 74 optimal weight:   50.0000
   overall best weight:    2.4788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
C  68 ASN
C  89 ASN
C 112 GLN
D  92 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
G 104 GLN
H  79 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.077438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.056515 restraints weight = 37849.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058329 restraints weight = 18774.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.059568 restraints weight = 12342.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.060356 restraints weight = 9570.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.060742 restraints weight = 8266.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10893  Z= 0.175
  Angle     :  0.745   9.672  15464  Z= 0.427
  Chirality :  0.048   0.246   1715
  Planarity :  0.005   0.045   1327
  Dihedral  : 29.770  89.900   3109
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.95 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.78 (0.26), residues: 829
  helix: -0.09 (0.20), residues: 580
  sheet:  None (None), residues: 0
  loop : -1.28 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  83 
 TYR   0.023   0.002   TYR D  80 
 PHE   0.007   0.001   PHE B 100 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.18 (10892)
  covalent geometry    : angle       0.74506 /  0.43 (15464)
  hydrogen bonds       : bond        0.04980 /  3.25 (  624)
  hydrogen bonds       : angle       3.60907 /  2.49 ( 1641)
  Misc. bond           : bond        0.00829 /  0.44 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 261
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9322 (tt0) cc_final: 0.8884 (tm-30)
REVERT: B   20 LYS cc_start: 0.7321 (mmmm) cc_final: 0.7111 (mmmm)
REVERT: B   25 ASN cc_start: 0.8546 (m-40) cc_final: 0.8203 (t0)
REVERT: B   27 GLN cc_start: 0.8689 (mp10) cc_final: 0.8461 (mp10)
REVERT: B   92 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7724 (ttp80)
REVERT: C   64 GLU cc_start: 0.8506 (tt0) cc_final: 0.7717 (tm-30)
REVERT: C   73 ASN cc_start: 0.9149 (t0) cc_final: 0.8757 (t0)
REVERT: C   84 GLN cc_start: 0.8677 (tp40) cc_final: 0.8214 (tp40)
REVERT: C   92 GLU cc_start: 0.8191 (pm20) cc_final: 0.7873 (pm20)
REVERT: C  104 GLN cc_start: 0.8261 (tp-100) cc_final: 0.8060 (tp-100)
REVERT: D   68 GLU cc_start: 0.8894 (tp30) cc_final: 0.8592 (tp30)
REVERT: D   77 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8692 (mp)
REVERT: D   90 GLU cc_start: 0.9231 (mp0) cc_final: 0.8654 (mp0)
REVERT: E   86 SER cc_start: 0.8854 (m) cc_final: 0.8647 (p)
REVERT: E  125 GLN cc_start: 0.9038 (mm110) cc_final: 0.8741 (mm110)
REVERT: F   88 TYR cc_start: 0.8834 (m-10) cc_final: 0.7872 (m-10)
REVERT: G   56 GLU cc_start: 0.8957 (tt0) cc_final: 0.8357 (tt0)
REVERT: H   73 GLU cc_start: 0.8685 (mm-30) cc_final: 0.7912 (mm-30)
REVERT: H   83 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.7908 (mmt-90)
REVERT: H   85 THR cc_start: 0.9044 (m) cc_final: 0.8501 (p)
REVERT: H   96 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8661 (mtp85)
REVERT: H  117 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9030 (mtmt)
  outliers start: 18
  outliers final: 8
  residues processed: 268
  average time/residue: 0.1141
  time to fit residues: 41.2302
Evaluate side-chains
  241 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 232
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  104 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:   50.0000
   chunk 22 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:   50.0000
   chunk 77 optimal weight:   40.0000
   overall best weight:    1.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
C  89 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.077017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.055927 restraints weight = 38139.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.057763 restraints weight = 19195.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.058987 restraints weight = 12692.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.059761 restraints weight = 9900.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.060218 restraints weight = 8580.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10893  Z= 0.157
  Angle     :  0.688   9.879  15464  Z= 0.399
  Chirality :  0.045   0.245   1715
  Planarity :  0.004   0.059   1327
  Dihedral  : 29.542  89.551   3109
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.68 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.26 (0.27), residues: 829
  helix:  0.76 (0.20), residues: 577
  sheet:  None (None), residues: 0
  loop : -1.07 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  29 
 TYR   0.029   0.002   TYR F  98 
 PHE   0.017   0.001   PHE E  84 
 HIS   0.005   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.16 (10892)
  covalent geometry    : angle       0.68801 /  0.40 (15464)
  hydrogen bonds       : bond        0.04583 /  3.03 (  624)
  hydrogen bonds       : angle       3.43764 /  2.36 ( 1641)
  Misc. bond           : bond        0.00375 /  0.20 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 247
  time to evaluate  : 0.315 
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   50 GLU cc_start: 0.9245 (tt0) cc_final: 0.8866 (tm-30)
REVERT: B   63 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8682 (mm-30)
REVERT: B   92 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7804 (ttp80)
REVERT: C   64 GLU cc_start: 0.8487 (tt0) cc_final: 0.7949 (tm-30)
REVERT: C   68 ASN cc_start: 0.8719 (m-40) cc_final: 0.8216 (t0)
REVERT: C   72 ASP cc_start: 0.7896 (m-30) cc_final: 0.7192 (m-30)
REVERT: C   73 ASN cc_start: 0.9092 (t0) cc_final: 0.8761 (t0)
REVERT: C   84 GLN cc_start: 0.8647 (tp40) cc_final: 0.8212 (tp40)
REVERT: C   92 GLU cc_start: 0.8166 (pm20) cc_final: 0.7750 (pm20)
REVERT: D   68 GLU cc_start: 0.8854 (tp30) cc_final: 0.8615 (tp30)
REVERT: D   77 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8807 (mp)
REVERT: D   90 GLU cc_start: 0.9174 (mp0) cc_final: 0.8611 (mp0)
REVERT: D  102 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: D  105 LYS cc_start: 0.9204 (ptpp) cc_final: 0.8763 (ptpp)
REVERT: E   50 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8448 (mm-30)
REVERT: E   56 LYS cc_start: 0.9334 (mtpp) cc_final: 0.9035 (mtmm)
REVERT: E  125 GLN cc_start: 0.8981 (mm110) cc_final: 0.8730 (mm110)
REVERT: F   63 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8191 (mt-10)
REVERT: F   88 TYR cc_start: 0.8603 (m-10) cc_final: 0.8152 (m-10)
REVERT: F   98 TYR cc_start: 0.8663 (m-80) cc_final: 0.8246 (m-80)
REVERT: G   56 GLU cc_start: 0.8905 (tt0) cc_final: 0.8329 (tt0)
REVERT: G   68 ASN cc_start: 0.8965 (m-40) cc_final: 0.8701 (m-40)
REVERT: H   37 TYR cc_start: 0.8984 (m-80) cc_final: 0.8769 (m-80)
REVERT: H   73 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8361 (tp30)
REVERT: H   83 ARG cc_start: 0.8508 (mmt-90) cc_final: 0.7921 (mmt-90)
REVERT: H   85 THR cc_start: 0.9108 (m) cc_final: 0.8579 (p)
REVERT: H   96 ARG cc_start: 0.8876 (mtp85) cc_final: 0.8670 (mtp85)
REVERT: H  117 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9157 (mtmt)
  outliers start: 17
  outliers final: 9
  residues processed: 253
  average time/residue: 0.1193
  time to fit residues: 40.9028
Evaluate side-chains
  237 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 227
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   30 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 36 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 63 optimal weight:    8.9990
   chunk 73 optimal weight:   50.0000
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    3.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.076386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.055121 restraints weight = 38419.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.056923 restraints weight = 19189.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.058099 restraints weight = 12717.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.058848 restraints weight = 9993.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.059299 restraints weight = 8688.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10893  Z= 0.176
  Angle     :  0.678   7.699  15464  Z= 0.392
  Chirality :  0.044   0.242   1715
  Planarity :  0.004   0.032   1327
  Dihedral  : 29.439  89.052   3109
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.53 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.02 (0.28), residues: 829
  helix:  1.47 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop : -0.99 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  76 
 TYR   0.019   0.002   TYR A  99 
 PHE   0.008   0.001   PHE E  78 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.18 (10892)
  covalent geometry    : angle       0.67807 /  0.39 (15464)
  hydrogen bonds       : bond        0.04508 /  2.97 (  624)
  hydrogen bonds       : angle       3.31204 /  2.28 ( 1641)
  Misc. bond           : bond        0.01226 /  0.65 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 233
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9282 (tt0) cc_final: 0.8875 (tm-30)
REVERT: B   63 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8705 (mm-30)
REVERT: B   67 ARG cc_start: 0.9292 (ttp80) cc_final: 0.9040 (ttm110)
REVERT: B   88 TYR cc_start: 0.7760 (m-10) cc_final: 0.7491 (m-10)
REVERT: B   92 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7718 (ttp80)
REVERT: C   64 GLU cc_start: 0.8501 (tt0) cc_final: 0.7903 (tm-30)
REVERT: C   73 ASN cc_start: 0.9102 (t0) cc_final: 0.8735 (t0)
REVERT: C   84 GLN cc_start: 0.8574 (tp40) cc_final: 0.8168 (tp40)
REVERT: C  104 GLN cc_start: 0.8533 (mm-40) cc_final: 0.7691 (mm-40)
REVERT: D   77 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8827 (mp)
REVERT: D   90 GLU cc_start: 0.9231 (mp0) cc_final: 0.8605 (mp0)
REVERT: D  102 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8086 (mm-30)
REVERT: D  105 LYS cc_start: 0.9235 (ptpp) cc_final: 0.8725 (ptpp)
REVERT: E   50 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8462 (mm-30)
REVERT: E   56 LYS cc_start: 0.9323 (mtpp) cc_final: 0.9076 (mtmm)
REVERT: F   63 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8214 (mt-10)
REVERT: F   88 TYR cc_start: 0.8593 (m-10) cc_final: 0.8228 (m-10)
REVERT: G   41 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8116 (mp0)
REVERT: G   56 GLU cc_start: 0.8939 (tt0) cc_final: 0.8363 (tt0)
REVERT: G   64 GLU cc_start: 0.8511 (tp30) cc_final: 0.7657 (tp30)
REVERT: G   68 ASN cc_start: 0.8985 (m-40) cc_final: 0.8643 (m-40)
REVERT: H   37 TYR cc_start: 0.9008 (m-80) cc_final: 0.8808 (m-80)
REVERT: H   73 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8314 (mm-30)
REVERT: H   83 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8141 (mmt-90)
REVERT: H   85 THR cc_start: 0.9138 (m) cc_final: 0.8658 (p)
REVERT: H  117 LYS cc_start: 0.9397 (mtmt) cc_final: 0.9148 (mtmt)
  outliers start: 26
  outliers final: 14
  residues processed: 242
  average time/residue: 0.1242
  time to fit residues: 40.6139
Evaluate side-chains
  237 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 222
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 74 optimal weight:   50.0000
   chunk 81 optimal weight:   50.0000
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 4 optimal weight:   20.0000
   chunk 53 optimal weight:   20.0000
   chunk 39 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   overall best weight:    3.8588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.075715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.054287 restraints weight = 38251.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.056101 restraints weight = 19267.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.057287 restraints weight = 12750.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058024 restraints weight = 10029.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.058474 restraints weight = 8736.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  10893  Z= 0.175
  Angle     :  0.666   7.837  15464  Z= 0.388
  Chirality :  0.044   0.245   1715
  Planarity :  0.004   0.032   1327
  Dihedral  : 29.373  88.935   3109
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.46 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.43 (0.28), residues: 829
  helix:  1.75 (0.21), residues: 565
  sheet:  None (None), residues: 0
  loop : -0.80 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  40 
 TYR   0.023   0.002   TYR D  80 
 PHE   0.009   0.001   PHE E  84 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.17 (10892)
  covalent geometry    : angle       0.66641 /  0.39 (15464)
  hydrogen bonds       : bond        0.04447 /  2.94 (  624)
  hydrogen bonds       : angle       3.25569 /  2.25 ( 1641)
  Misc. bond           : bond        0.00303 /  0.16 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 240
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9311 (tt0) cc_final: 0.8882 (tm-30)
REVERT: B   53 GLU cc_start: 0.9045 (tp30) cc_final: 0.8841 (tp30)
REVERT: B   63 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8747 (mm-30)
REVERT: B   67 ARG cc_start: 0.9325 (ttp80) cc_final: 0.9061 (ttm110)
REVERT: B   92 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7718 (ttp80)
REVERT: C   64 GLU cc_start: 0.8499 (tt0) cc_final: 0.8001 (tm-30)
REVERT: C   73 ASN cc_start: 0.9094 (t0) cc_final: 0.8716 (t0)
REVERT: C   84 GLN cc_start: 0.8544 (tp40) cc_final: 0.8127 (tp40)
REVERT: C   92 GLU cc_start: 0.8071 (pm20) cc_final: 0.7845 (pm20)
REVERT: C  104 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7671 (mm-40)
REVERT: D   90 GLU cc_start: 0.9294 (mp0) cc_final: 0.8604 (mp0)
REVERT: D  105 LYS cc_start: 0.9219 (ptpp) cc_final: 0.8816 (ptpp)
REVERT: E   56 LYS cc_start: 0.9338 (mtpp) cc_final: 0.9010 (mtmm)
REVERT: E  117 VAL cc_start: 0.9092 (m) cc_final: 0.8886 (p)
REVERT: F   88 TYR cc_start: 0.8656 (m-10) cc_final: 0.7417 (m-10)
REVERT: G   41 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8244 (mp0)
REVERT: G   56 GLU cc_start: 0.8955 (tt0) cc_final: 0.8380 (tt0)
REVERT: H   80 TYR cc_start: 0.8594 (m-10) cc_final: 0.7966 (m-10)
REVERT: H   83 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8184 (mmt-90)
REVERT: H   85 THR cc_start: 0.9075 (m) cc_final: 0.8624 (p)
REVERT: H  117 LYS cc_start: 0.9444 (mtmt) cc_final: 0.9212 (mtmt)
  outliers start: 26
  outliers final: 17
  residues processed: 251
  average time/residue: 0.1188
  time to fit residues: 40.2307
Evaluate side-chains
  241 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 224
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 76 optimal weight:   40.0000
   chunk 75 optimal weight:   40.0000
   chunk 73 optimal weight:   50.0000
   chunk 71 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 80 optimal weight:   50.0000
   chunk 64 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
C  68 ASN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.074087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.052514 restraints weight = 38808.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.054269 restraints weight = 19732.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.055418 restraints weight = 13221.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.056132 restraints weight = 10443.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.056576 restraints weight = 9132.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10893  Z= 0.215
  Angle     :  0.709  11.147  15464  Z= 0.403
  Chirality :  0.045   0.246   1715
  Planarity :  0.004   0.036   1327
  Dihedral  : 29.357  88.928   3109
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 22.71 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.73 (0.28), residues: 829
  helix:  1.95 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.64 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  35 
 TYR   0.022   0.003   TYR D  80 
 PHE   0.009   0.002   PHE E  78 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.22 (10892)
  covalent geometry    : angle       0.70942 /  0.40 (15464)
  hydrogen bonds       : bond        0.04894 /  3.25 (  624)
  hydrogen bonds       : angle       3.30321 /  2.29 ( 1641)
  Misc. bond           : bond        0.00259 /  0.14 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9322 (tt0) cc_final: 0.8987 (tp30)
REVERT: B   63 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8750 (mm-30)
REVERT: B   92 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7867 (ttp80)
REVERT: C   73 ASN cc_start: 0.9113 (t0) cc_final: 0.8773 (t0)
REVERT: C   84 GLN cc_start: 0.8607 (tp40) cc_final: 0.8182 (tp40)
REVERT: C  104 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7762 (mm-40)
REVERT: D   35 SER cc_start: 0.9426 (m) cc_final: 0.9219 (t)
REVERT: D   90 GLU cc_start: 0.9293 (mp0) cc_final: 0.8628 (mp0)
REVERT: D  102 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8093 (mm-30)
REVERT: D  105 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8943 (ptpp)
REVERT: E   56 LYS cc_start: 0.9361 (mtpp) cc_final: 0.9030 (mtmm)
REVERT: F   88 TYR cc_start: 0.8679 (m-10) cc_final: 0.7204 (m-10)
REVERT: G   56 GLU cc_start: 0.8964 (tt0) cc_final: 0.8410 (tt0)
REVERT: H   73 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8339 (tp30)
REVERT: H   80 TYR cc_start: 0.8678 (m-10) cc_final: 0.8102 (m-10)
REVERT: H   85 THR cc_start: 0.9082 (m) cc_final: 0.8606 (p)
REVERT: H  117 LYS cc_start: 0.9445 (mtmt) cc_final: 0.9223 (mtmt)
  outliers start: 29
  outliers final: 20
  residues processed: 234
  average time/residue: 0.1149
  time to fit residues: 36.6629
Evaluate side-chains
  237 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 216
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue  105 LYS
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 87 optimal weight:   50.0000
   chunk 83 optimal weight:   40.0000
   chunk 42 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 93 optimal weight:   30.0000
   chunk 43 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
C  68 ASN
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.075608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.054672 restraints weight = 37323.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.056462 restraints weight = 18598.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.057665 restraints weight = 12283.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058405 restraints weight = 9613.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.058876 restraints weight = 8334.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10893  Z= 0.145
  Angle     :  0.681   8.148  15464  Z= 0.392
  Chirality :  0.045   0.248   1715
  Planarity :  0.004   0.031   1327
  Dihedral  : 29.258  89.018   3109
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 24.42 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.80 (0.28), residues: 829
  helix:  2.03 (0.21), residues: 565
  sheet:  None (None), residues: 0
  loop : -0.64 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  40 
 TYR   0.032   0.002   TYR B  88 
 PHE   0.008   0.001   PHE E  78 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.14 (10892)
  covalent geometry    : angle       0.68090 /  0.39 (15464)
  hydrogen bonds       : bond        0.04211 /  2.80 (  624)
  hydrogen bonds       : angle       3.20970 /  2.21 ( 1641)
  Misc. bond           : bond        0.00088 /  0.05 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 240
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9303 (tt0) cc_final: 0.8904 (tm-30)
REVERT: B   63 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8740 (mm-30)
REVERT: B   92 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7835 (ttp80)
REVERT: B   98 TYR cc_start: 0.9108 (m-10) cc_final: 0.8902 (m-80)
REVERT: C   27 VAL cc_start: 0.8974 (m) cc_final: 0.8773 (p)
REVERT: C   64 GLU cc_start: 0.8582 (tt0) cc_final: 0.7984 (tm-30)
REVERT: C   68 ASN cc_start: 0.9035 (m-40) cc_final: 0.8800 (m110)
REVERT: C   73 ASN cc_start: 0.9090 (t0) cc_final: 0.8760 (t0)
REVERT: C   84 GLN cc_start: 0.8490 (tp40) cc_final: 0.8056 (tp40)
REVERT: C   92 GLU cc_start: 0.7975 (pm20) cc_final: 0.7466 (pm20)
REVERT: C  104 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7727 (mm-40)
REVERT: D   35 SER cc_start: 0.9446 (m) cc_final: 0.9208 (t)
REVERT: D   56 MET cc_start: 0.8718 (tpp) cc_final: 0.8318 (tpt)
REVERT: D   90 GLU cc_start: 0.9262 (mp0) cc_final: 0.8603 (mp0)
REVERT: D  102 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: E   56 LYS cc_start: 0.9331 (mtpp) cc_final: 0.9061 (mtmm)
REVERT: F   53 GLU cc_start: 0.8390 (tt0) cc_final: 0.8115 (tt0)
REVERT: F   60 VAL cc_start: 0.9458 (p) cc_final: 0.8783 (m)
REVERT: F   63 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8249 (mt-10)
REVERT: F   88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8087 (m-10)
REVERT: G   56 GLU cc_start: 0.8923 (tt0) cc_final: 0.8390 (tt0)
REVERT: G  104 GLN cc_start: 0.8437 (mp10) cc_final: 0.8159 (mp10)
REVERT: H   54 LYS cc_start: 0.8743 (ptmt) cc_final: 0.8500 (ptmt)
REVERT: H   73 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7721 (mm-30)
REVERT: H   85 THR cc_start: 0.8758 (m) cc_final: 0.8005 (p)
REVERT: H  117 LYS cc_start: 0.9442 (mtmt) cc_final: 0.9114 (mtmt)
  outliers start: 22
  outliers final: 12
  residues processed: 250
  average time/residue: 0.1155
  time to fit residues: 39.3445
Evaluate side-chains
  235 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 223
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 91 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.074425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.053378 restraints weight = 38045.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.055152 restraints weight = 19125.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.056338 restraints weight = 12712.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.057067 restraints weight = 9960.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.057492 restraints weight = 8655.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10893  Z= 0.191
  Angle     :  0.716   9.643  15464  Z= 0.405
  Chirality :  0.045   0.250   1715
  Planarity :  0.004   0.052   1327
  Dihedral  : 29.282  89.327   3109
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 26.13 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.96 (0.29), residues: 829
  helix:  2.08 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop : -0.45 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  76 
 TYR   0.068   0.003   TYR B  88 
 PHE   0.010   0.001   PHE E  78 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.19 (10892)
  covalent geometry    : angle       0.71613 /  0.41 (15464)
  hydrogen bonds       : bond        0.04586 /  3.04 (  624)
  hydrogen bonds       : angle       3.31678 /  2.28 ( 1641)
  Misc. bond           : bond        0.00112 /  0.06 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 223
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7686 (m-80) cc_final: 0.6574 (m-80)
REVERT: A   50 GLU cc_start: 0.9304 (tt0) cc_final: 0.8893 (tm-30)
REVERT: B   53 GLU cc_start: 0.9115 (tp30) cc_final: 0.8780 (tp30)
REVERT: B   63 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8757 (mm-30)
REVERT: B   92 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7786 (ttp80)
REVERT: C   64 GLU cc_start: 0.8673 (tt0) cc_final: 0.8048 (tm-30)
REVERT: C   68 ASN cc_start: 0.9015 (m-40) cc_final: 0.8811 (m110)
REVERT: C   73 ASN cc_start: 0.9066 (t0) cc_final: 0.8725 (t0)
REVERT: C   84 GLN cc_start: 0.8555 (tp40) cc_final: 0.8100 (tp40)
REVERT: C  104 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7775 (mm-40)
REVERT: D   35 SER cc_start: 0.9452 (m) cc_final: 0.9201 (t)
REVERT: D   90 GLU cc_start: 0.9289 (mp0) cc_final: 0.8613 (mp0)
REVERT: E   94 GLU cc_start: 0.8864 (tp30) cc_final: 0.8633 (tp30)
REVERT: F   88 TYR cc_start: 0.8736 (m-10) cc_final: 0.7167 (m-10)
REVERT: G   56 GLU cc_start: 0.8946 (tt0) cc_final: 0.8405 (tt0)
REVERT: G   61 GLU cc_start: 0.8976 (tp30) cc_final: 0.8692 (tp30)
REVERT: G   75 LYS cc_start: 0.9235 (mmmm) cc_final: 0.9002 (mptt)
REVERT: H   73 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8129 (tp30)
REVERT: H   80 TYR cc_start: 0.8615 (m-10) cc_final: 0.8099 (m-10)
REVERT: H   83 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8374 (tpp-160)
REVERT: H   85 THR cc_start: 0.8755 (m) cc_final: 0.8102 (p)
REVERT: H  117 LYS cc_start: 0.9457 (mtmt) cc_final: 0.9137 (mtmt)
  outliers start: 17
  outliers final: 12
  residues processed: 228
  average time/residue: 0.1124
  time to fit residues: 34.7288
Evaluate side-chains
  225 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 213
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 84 optimal weight:   50.0000
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 81 optimal weight:   50.0000
   chunk 58 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    5.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.074007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.053018 restraints weight = 37870.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.054779 restraints weight = 18990.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.055946 restraints weight = 12619.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.056686 restraints weight = 9891.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.057134 restraints weight = 8587.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10893  Z= 0.208
  Angle     :  0.738  13.073  15464  Z= 0.414
  Chirality :  0.045   0.250   1715
  Planarity :  0.004   0.033   1327
  Dihedral  : 29.306  89.182   3109
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 27.06 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.95 (0.28), residues: 829
  helix:  2.05 (0.21), residues: 571
  sheet:  None (None), residues: 0
  loop : -0.41 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  76 
 TYR   0.067   0.003   TYR B  88 
 PHE   0.008   0.001   PHE E  84 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.21 (10892)
  covalent geometry    : angle       0.73815 /  0.41 (15464)
  hydrogen bonds       : bond        0.04687 /  3.11 (  624)
  hydrogen bonds       : angle       3.37608 /  2.32 ( 1641)
  Misc. bond           : bond        0.00125 /  0.07 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9308 (tt0) cc_final: 0.8898 (tm-30)
REVERT: B   53 GLU cc_start: 0.9132 (tp30) cc_final: 0.8802 (tp30)
REVERT: B   63 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8766 (mm-30)
REVERT: B   92 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7913 (ttp80)
REVERT: C   64 GLU cc_start: 0.8675 (tt0) cc_final: 0.7952 (tm-30)
REVERT: C   68 ASN cc_start: 0.9028 (m-40) cc_final: 0.8645 (m110)
REVERT: C   73 ASN cc_start: 0.9043 (t0) cc_final: 0.8736 (t0)
REVERT: C   84 GLN cc_start: 0.8569 (tp40) cc_final: 0.8121 (tp-100)
REVERT: C  104 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7824 (mm-40)
REVERT: D   35 SER cc_start: 0.9384 (m) cc_final: 0.9150 (t)
REVERT: D   90 GLU cc_start: 0.9292 (mp0) cc_final: 0.8608 (mp0)
REVERT: D  117 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9080 (mtpt)
REVERT: E   56 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9107 (mtmm)
REVERT: E   94 GLU cc_start: 0.8844 (tp30) cc_final: 0.8629 (tp30)
REVERT: F   53 GLU cc_start: 0.8462 (tt0) cc_final: 0.8245 (tt0)
REVERT: F   88 TYR cc_start: 0.8706 (m-10) cc_final: 0.7179 (m-10)
REVERT: G   56 GLU cc_start: 0.8936 (tt0) cc_final: 0.8408 (tt0)
REVERT: G   61 GLU cc_start: 0.8976 (tp30) cc_final: 0.8730 (tp30)
REVERT: G  104 GLN cc_start: 0.8298 (mp10) cc_final: 0.7780 (mp10)
REVERT: H   73 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8103 (tp30)
REVERT: H   80 TYR cc_start: 0.8615 (m-10) cc_final: 0.8143 (m-10)
REVERT: H   83 ARG cc_start: 0.8632 (tpp-160) cc_final: 0.8397 (tpp-160)
REVERT: H   85 THR cc_start: 0.8775 (m) cc_final: 0.8157 (p)
REVERT: H  117 LYS cc_start: 0.9459 (mtmt) cc_final: 0.9142 (mtmt)
  outliers start: 17
  outliers final: 13
  residues processed: 227
  average time/residue: 0.1159
  time to fit residues: 35.6209
Evaluate side-chains
  228 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 215
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 7 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0050
   chunk 17 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:   50.0000
   chunk 36 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.2002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.075109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.054101 restraints weight = 37352.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.055907 restraints weight = 18659.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.057099 restraints weight = 12355.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.057856 restraints weight = 9675.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.058274 restraints weight = 8389.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10893  Z= 0.157
  Angle     :  0.733  12.498  15464  Z= 0.410
  Chirality :  0.044   0.252   1715
  Planarity :  0.004   0.033   1327
  Dihedral  : 29.261  89.358   3109
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 27.53 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.03 (0.29), residues: 829
  helix:  2.10 (0.21), residues: 571
  sheet:  None (None), residues: 0
  loop : -0.36 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D  76 
 TYR   0.052   0.003   TYR D  80 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.16 (10892)
  covalent geometry    : angle       0.73344 /  0.41 (15464)
  hydrogen bonds       : bond        0.04282 /  2.84 (  624)
  hydrogen bonds       : angle       3.30529 /  2.27 ( 1641)
  Misc. bond           : bond        0.00133 /  0.07 (    1)

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

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

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1658 Ramachandran restraints generated.
    829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 230
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.9157 (tp30) cc_final: 0.8814 (tp30)
REVERT: B   63 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8814 (mm-30)
REVERT: B   92 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7897 (ttp80)
REVERT: B   98 TYR cc_start: 0.9113 (m-10) cc_final: 0.8913 (m-80)
REVERT: C   36 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9095 (mmmm)
REVERT: C   64 GLU cc_start: 0.8666 (tt0) cc_final: 0.7850 (tm-30)
REVERT: C   68 ASN cc_start: 0.9029 (m-40) cc_final: 0.8645 (m110)
REVERT: C   73 ASN cc_start: 0.9019 (t0) cc_final: 0.8705 (t0)
REVERT: C   84 GLN cc_start: 0.8488 (tp40) cc_final: 0.7999 (tp40)
REVERT: C  104 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7777 (mm-40)
REVERT: D   90 GLU cc_start: 0.9292 (mp0) cc_final: 0.8602 (mp0)
REVERT: E   56 LYS cc_start: 0.9377 (mtpp) cc_final: 0.9104 (mtmm)
REVERT: E   94 GLU cc_start: 0.8831 (tp30) cc_final: 0.8629 (tp30)
REVERT: G   56 GLU cc_start: 0.8930 (tt0) cc_final: 0.8380 (tt0)
REVERT: G   61 GLU cc_start: 0.9019 (tp30) cc_final: 0.8750 (tp30)
REVERT: G   75 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8960 (mptt)
REVERT: G  104 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7619 (mp10)
REVERT: H   73 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7975 (tp30)
REVERT: H   83 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8311 (tpp-160)
REVERT: H   85 THR cc_start: 0.8753 (m) cc_final: 0.8152 (p)
REVERT: H  117 LYS cc_start: 0.9465 (mtmt) cc_final: 0.9136 (mtmt)
  outliers start: 13
  outliers final: 9
  residues processed: 234
  average time/residue: 0.1168
  time to fit residues: 36.9128
Evaluate side-chains
  231 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 221
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue  104 GLN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   48 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   chunk 70 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 45 optimal weight:    0.1980
   chunk 59 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    1.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 106 HIS
E  68 GLN
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.075095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.053999 restraints weight = 37661.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.055785 restraints weight = 18871.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.056966 restraints weight = 12538.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.057716 restraints weight = 9834.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.058159 restraints weight = 8543.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10893  Z= 0.158
  Angle     :  0.738  14.227  15464  Z= 0.412
  Chirality :  0.044   0.253   1715
  Planarity :  0.004   0.055   1327
  Dihedral  : 29.240  89.620   3109
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 28.30 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.00 (0.29), residues: 829
  helix:  1.99 (0.21), residues: 583
  sheet:  None (None), residues: 0
  loop : -0.25 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  76 
 TYR   0.084   0.003   TYR D  80 
 PHE   0.012   0.001   PHE E  78 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.16 (10892)
  covalent geometry    : angle       0.73823 /  0.41 (15464)
  hydrogen bonds       : bond        0.04287 /  2.84 (  624)
  hydrogen bonds       : angle       3.34327 /  2.30 ( 1641)
  Misc. bond           : bond        0.00085 /  0.04 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1788.91 seconds
wall clock time: 31 minutes 33.25 seconds (1893.25 seconds total)