Starting phenix.real_space_refine
on Sat Aug 23 02:55:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f0x_50117/08_2025/9f0x_50117.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f0x_50117/08_2025/9f0x_50117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_2025/9f0x_50117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_2025/9f0x_50117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_2025/9f0x_50117.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_2025/9f0x_50117.cif"
  }
  resolution = 3.78
  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=   0.001 sd=   0.031
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     166      5.49       5
     S      22      5.16       5
     C    5408      2.51       5
     N    1700      2.21       5
     O    2127      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9423
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 1705
          Classifications: {'DNA': 83}
          Link IDs: {'rna3p': 82}
    Chain: "B"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 1698
          Classifications: {'DNA': 83}
          Link IDs: {'rna3p': 82}
    Chain: "C"
      Number of atoms: 759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 759
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 900
          Classifications: {'peptide': 113}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "F"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 49
          Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "G"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 764
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "H"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 1947
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 14, 'TRANS': 251}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 74
  Time building chain proxies: 1.86, per 1000 atoms: 0.20
  Number of scatterers: 9423
  At special positions: 0
  Unit cell: (94.05, 94.05, 183.15, 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      22     16.00
     P     166     15.00
     O    2127      8.00
     N    1700      7.00
     C    5408      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 203.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 11 sheets defined
      45.1% alpha, 16.6% beta
      77 base pairs and 142 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 17
    Processing helix  chain 'C' and resid 19 through 40
      removed outlier: 3.676A  pdb=" N   PHE C  31 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE C  34 " --> pdb=" O   PHE C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 90
    Processing helix  chain 'D' and resid 2 through 14
      removed outlier: 3.723A  pdb=" N   GLU D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 39
    Processing helix  chain 'D' and resid 83 through 91
    Processing helix  chain 'E' and resid 19 through 33
      removed outlier: 4.556A  pdb=" N   LEU E  25 " --> pdb=" O   ASP E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 52
      removed outlier: 3.622A  pdb=" N   ARG E  44 " --> pdb=" O   GLU E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 90
      removed outlier: 4.247A  pdb=" N   LEU E  81 " --> pdb=" O   GLU E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 108
    Processing helix  chain 'F' and resid 22 through 34
      removed outlier: 3.656A  pdb=" N   LEU F  26 " --> pdb=" O   VAL F  22 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 52
    Processing helix  chain 'F' and resid 75 through 90
    Processing helix  chain 'F' and resid 92 through 108
    Processing helix  chain 'G' and resid 19 through 34
      removed outlier: 4.807A  pdb=" N   LEU G  25 " --> pdb=" O   ASP G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 52
      removed outlier: 4.184A  pdb=" N   LEU G  49 " --> pdb=" O   LEU G  45 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   HIS G  50 " --> pdb=" O   LYS G  46 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG G  51 " --> pdb=" O   ASP G  47 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   TYR G  52 " --> pdb=" O   HIS G  48 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 61 through 65
    Processing helix  chain 'G' and resid 75 through 90
      removed outlier: 3.794A  pdb=" N   ARG G  88 " --> pdb=" O   ALA G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 108
      removed outlier: 3.771A  pdb=" N   LYS G 107 " --> pdb=" O   ASP G 103 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 577 through 594
      removed outlier: 3.627A  pdb=" N   ALA H 581 " --> pdb=" O   ASN H 577 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG H 582 " --> pdb=" O   VAL H 578 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 604 through 622
    Processing helix  chain 'H' and resid 646 through 650
    Processing helix  chain 'H' and resid 696 through 698
      No H-bonds generated for 'chain 'H' and resid 696 through 698'
    Processing helix  chain 'H' and resid 763 through 767
    Processing helix  chain 'H' and resid 793 through 797
      removed outlier: 3.576A  pdb=" N   MET H 797 " --> pdb=" O   GLN H 794 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 798 through 808
    Processing helix  chain 'H' and resid 821 through 825
      removed outlier: 3.524A  pdb=" N   GLU H 825 " --> pdb=" O   ARG H 822 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46
      removed outlier: 4.064A  pdb=" N   VAL C  44 " --> pdb=" O   PHE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 57
    Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 61
      removed outlier: 3.713A  pdb=" N   ARG C  60 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 43 through 45
    Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 62
    Processing sheet with id=AA6, first strand: chain 'E' and resid 13 through 18
    Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 19
    Processing sheet with id=AA8, first strand: chain 'G' and resid 13 through 18
    Processing sheet with id=AA9, first strand: chain 'H' and resid 568 through 572
      removed outlier: 3.540A  pdb=" N   ALA H 790 " --> pdb=" O   ARG H 813 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL H 598 " --> pdb=" O   PHE H 789 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   SER H 791 " --> pdb=" O   VAL H 598 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLN H 600 " --> pdb=" O   SER H 791 " (cutoff:3.500A)
      removed outlier: 9.209A  pdb=" N   GLU H 776 " --> pdb=" O   SER H 597 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ALA H 599 " --> pdb=" O   GLU H 776 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 632 through 637
      removed outlier: 4.572A  pdb=" N   LEU H 704 " --> pdb=" O   VAL H 637 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   THR H 682 " --> pdb=" O   ASP H 672 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   VAL H 674 " --> pdb=" O   SER H 680 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   SER H 680 " --> pdb=" O   VAL H 674 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 756 through 759
      removed outlier: 3.864A  pdb=" N   SER H 739 " --> pdb=" O   THR H 746 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL H 748 " --> pdb=" O   VAL H 737 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL H 737 " --> pdb=" O   VAL H 748 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      171 hydrogen bonds
      342 hydrogen bond angles
      0 basepair planarities
      77 basepair parallelities
      142 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 0.80 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: 1735
        1.33 -     1.45: 3012
        1.45 -     1.57: 4814
        1.57 -     1.68: 330
        1.68 -     1.80: 41
  Bond restraints: 9932
  Sorted by residual:
  bond pdb=" C   PHE C  81 "
       pdb=" N   ARG C  82 "
    ideal  model  delta    sigma   weight residual
    1.332  1.306  0.025 8.60e-03 1.35e+04 8.75e+00
  bond pdb=" C   TYR H 650 "
       pdb=" N   ARG H 651 "
    ideal  model  delta    sigma   weight residual
    1.332  1.302  0.030 1.92e-02 2.71e+03 2.37e+00
  bond pdb=" C   ARG H 576 "
       pdb=" N   ASN H 577 "
    ideal  model  delta    sigma   weight residual
    1.332  1.313  0.019 1.40e-02 5.10e+03 1.90e+00
  bond pdb=" CA  ARG E  73 "
       pdb=" CB  ARG E  73 "
    ideal  model  delta    sigma   weight residual
    1.528  1.494  0.034 2.61e-02 1.47e+03 1.72e+00
  bond pdb=" C3'  DC B  75 "
       pdb=" C2'  DC B  75 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.00e-02 2.50e+03 1.65e+00
  ... (remaining 9927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 13485
        1.42 -     2.84: 609
        2.84 -     4.27: 44
        4.27 -     5.69: 6
        5.69 -     7.11: 2
  Bond angle restraints: 14146
  Sorted by residual:
  angle pdb=" C   TYR H 650 "
        pdb=" N   ARG H 651 "
        pdb=" CA  ARG H 651 "
      ideal   model   delta    sigma   weight residual
     122.31  115.20    7.11 2.34e+00 1.83e-01 9.24e+00
  angle pdb=" N   PHE C  49 "
        pdb=" CA  PHE C  49 "
        pdb=" C   PHE C  49 "
      ideal   model   delta    sigma   weight residual
     113.18  109.18    4.00 1.33e+00 5.65e-01 9.05e+00
  angle pdb=" N   PHE E   4 "
        pdb=" CA  PHE E   4 "
        pdb=" C   PHE E   4 "
      ideal   model   delta    sigma   weight residual
     114.75  111.39    3.36 1.26e+00 6.30e-01 7.11e+00
  angle pdb=" C3'  DT B  89 "
        pdb=" C2'  DT B  89 "
        pdb=" C1'  DT B  89 "
      ideal   model   delta    sigma   weight residual
     101.60   97.89    3.71 1.50e+00 4.44e-01 6.10e+00
  angle pdb=" N   GLY E   5 "
        pdb=" CA  GLY E   5 "
        pdb=" C   GLY E   5 "
      ideal   model   delta    sigma   weight residual
     113.18  118.46   -5.28 2.37e+00 1.78e-01 4.95e+00
  ... (remaining 14141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.29: 4901
       35.29 -    70.58: 759
       70.58 -   105.87: 12
      105.87 -   141.15: 1
      141.15 -   176.44: 1
  Dihedral angle restraints: 5674
    sinusoidal: 3384
      harmonic: 2290
  Sorted by residual:
  dihedral pdb=" C4'  DG B  47 "
           pdb=" C3'  DG B  47 "
           pdb=" O3'  DG B  47 "
           pdb=" P    DA B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.44 -176.44     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  LYS G  68 "
           pdb=" C   LYS G  68 "
           pdb=" N   TYR G  69 "
           pdb=" CA  TYR G  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  SER H 665 "
           pdb=" C   SER H 665 "
           pdb=" N   HIS H 666 "
           pdb=" CA  HIS H 666 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.01  -17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 5671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 966
       0.027 -    0.054: 431
       0.054 -    0.081: 137
       0.081 -    0.108: 55
       0.108 -    0.135: 19
  Chirality restraints: 1608
  Sorted by residual:
  chirality pdb=" P    DT B  91 "
            pdb=" OP1  DT B  91 "
            pdb=" OP2  DT B  91 "
            pdb=" O5'  DT B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" C4'  DA B  64 "
            pdb=" C5'  DA B  64 "
            pdb=" O4'  DA B  64 "
            pdb=" C3'  DA B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.39   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ILE D  17 "
            pdb=" N   ILE D  17 "
            pdb=" C   ILE D  17 "
            pdb=" CB  ILE D  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1605 not shown)

  Planarity restraints: 1241
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA A  63 "   -0.027 2.00e-02 2.50e+03   1.18e-02 3.80e+00
        pdb=" N9   DA A  63 "    0.024 2.00e-02 2.50e+03
        pdb=" C8   DA A  63 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA A  63 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA A  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA A  63 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA A  63 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA A  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA A  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA A  63 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  93 "    0.006 2.00e-02 2.50e+03   1.10e-02 3.01e+00
        pdb=" N1   DT A  93 "   -0.018 2.00e-02 2.50e+03
        pdb=" C2   DT A  93 "    0.021 2.00e-02 2.50e+03
        pdb=" O2   DT A  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DT A  93 "   -0.016 2.00e-02 2.50e+03
        pdb=" C4   DT A  93 "    0.010 2.00e-02 2.50e+03
        pdb=" O4   DT A  93 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DT A  93 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT A  93 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DT A  93 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B  61 "    0.023 2.00e-02 2.50e+03   1.02e-02 2.83e+00
        pdb=" N9   DA B  61 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA B  61 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA B  61 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA B  61 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA B  61 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA B  61 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA B  61 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA B  61 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DA B  61 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA B  61 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1238 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 127
        2.64 -     3.20: 8406
        3.20 -     3.77: 16879
        3.77 -     4.33: 21350
        4.33 -     4.90: 31138
  Nonbonded interactions: 77900
  Sorted by model distance:
  nonbonded pdb=" OP1  DT A  61 "
            pdb=" OG1 THR E   6 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" OP1  DG A  71 "
            pdb=" OG1 THR F   6 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER H 761 "
            pdb=" OG1 THR H 766 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" NE2 HIS F  48 "
            pdb=" OD2 ASP F 103 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OD1 ASP H 699 "
            pdb=" OG  SER H 701 "
     model   vdw
     2.201 3.040
  ... (remaining 77895 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 'E' and (resid 12 through 16 or (resid 17 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 18 through 22 or (resid 23 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 24 through 45 or (resid 46 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 47 or (resid 48 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 49 or (resid 50 t \ 
hrough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 t \ 
hrough 53 or (resid 54 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 55 or (resid 61 through 62 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 65 or (resid 66 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 67 through 73 or (resid 74 through 75 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 76 or (resid 77 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 78 or (resid 79 through 80 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 81 through 85 o \ 
r (resid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 \ 
 through 92 or (resid 93 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 94 or (resid 95 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 96 through 101 or (resid 102 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 103 through 107 or (resid 108 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 109 through 111 or (resid 112 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 113))
  selection = (chain 'F' and (resid 12 through 25 or (resid 26 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 27 or (resid 28 through 29 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 30 through 47 or (resid 48 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 49 through 55 or (r \ 
esid 61 through 62 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 63 through 65 or (resid 66 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 67 or (resid 68 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 69 through 73 or (resid 74 through 75 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 76 or (resid 77 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 78 or (resid 79 through 80 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 81 through 85 or (res \ 
id 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ 
gh 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 96 through 101 or (resid 102 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 103 through 107 or (resid 108 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 109 through 113))
  selection = (chain 'G' and (resid 12 through 22 or (resid 23 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 24 through 25 or (resid 26 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 27 or (resid 28 through 29 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 30 through 45 or (r \ 
esid 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thr \ 
ough 49 or (resid 50 through 51 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 52 through 67 or (resid 68 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 69 through 79 or (resid 80 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 81 through 111 or (resid 112 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 113))
}

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:             13.480
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.240
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
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      :  0.005   0.037   9932  Z= 0.245
  Angle     :  0.636   7.111  14146  Z= 0.381
  Chirality :  0.037   0.135   1608
  Planarity :  0.004   0.038   1241
  Dihedral  : 24.698 176.442   4184
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  2.91 %
    Favored  : 96.28 %
  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 aren not related in a simple way.
  whole: -0.09 (0.31), residues: 773
  helix:  1.10 (0.28), residues: 321
  sheet: -0.67 (0.41), residues: 155
  loop : -0.92 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  90 
 TYR   0.019   0.001   TYR H 669 
 PHE   0.021   0.002   PHE C  49 
 TRP   0.011   0.002   TRP H 774 
 HIS   0.002   0.001   HIS D  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 9932)
  covalent geometry    : angle       0.63589 (14146)
  hydrogen bonds       : bond        0.12746 (  485)
  hydrogen bonds       : angle       5.85956 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 212
  time to evaluate  : 0.273 
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: D    1 MET cc_start: 0.7020 (ttp) cc_final: 0.6163 (ptm)
REVERT: E   61 ILE cc_start: 0.8880 (mt) cc_final: 0.8678 (mm)
REVERT: E   95 ASP cc_start: 0.7720 (m-30) cc_final: 0.7416 (m-30)
REVERT: F   22 VAL cc_start: 0.8605 (m) cc_final: 0.8362 (p)
REVERT: G   39 PHE cc_start: 0.6983 (t80) cc_final: 0.6710 (t80)
REVERT: H  719 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7732 (mtm-85)
  outliers start: 5
  outliers final: 3
  residues processed: 216
  average time/residue: 0.0843
  time to fit residues: 24.8525
Evaluate side-chains
  137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  729 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
D  13 GLN
E  56 ASN
** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 691 GLN
H 803 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.072814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.059025 restraints weight = 49878.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.060415 restraints weight = 28844.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.061317 restraints weight = 20312.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.061848 restraints weight = 16159.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.062256 restraints weight = 13997.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9932  Z= 0.229
  Angle     :  0.683  11.188  14146  Z= 0.389
  Chirality :  0.038   0.149   1608
  Planarity :  0.005   0.036   1241
  Dihedral  : 28.604 169.583   2786
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.86 %
    Favored  : 81.26 %
  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 aren not related in a simple way.
  whole: -0.05 (0.30), residues: 773
  helix:  1.20 (0.28), residues: 330
  sheet: -0.52 (0.40), residues: 160
  loop : -1.14 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 100 
 TYR   0.011   0.001   TYR H 669 
 PHE   0.022   0.002   PHE F 117 
 TRP   0.014   0.001   TRP H 659 
 HIS   0.007   0.002   HIS E 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9932)
  covalent geometry    : angle       0.68318 (14146)
  hydrogen bonds       : bond        0.04857 (  485)
  hydrogen bonds       : angle       4.41435 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8748 (tp30) cc_final: 0.8142 (tm-30)
REVERT: C   92 GLU cc_start: 0.6233 (pm20) cc_final: 0.5832 (pm20)
REVERT: D   39 GLN cc_start: 0.8442 (tt0) cc_final: 0.8172 (tm-30)
REVERT: E    1 MET cc_start: 0.6768 (pmm) cc_final: 0.6428 (pmm)
REVERT: E   40 GLU cc_start: 0.7493 (tp30) cc_final: 0.7187 (tp30)
REVERT: E   61 ILE cc_start: 0.8758 (mt) cc_final: 0.8531 (tt)
REVERT: E   95 ASP cc_start: 0.7865 (m-30) cc_final: 0.7592 (m-30)
REVERT: F   24 SER cc_start: 0.9284 (t) cc_final: 0.9023 (p)
REVERT: F   72 MET cc_start: 0.7227 (ttm) cc_final: 0.6801 (tmm)
REVERT: F   81 LEU cc_start: 0.8802 (mm) cc_final: 0.7720 (mm)
REVERT: G   39 PHE cc_start: 0.7548 (t80) cc_final: 0.7181 (t80)
REVERT: H  813 ARG cc_start: 0.6717 (mpt180) cc_final: 0.6478 (mtp-110)
  outliers start: 24
  outliers final: 17
  residues processed: 153
  average time/residue: 0.0899
  time to fit residues: 18.6683
Evaluate side-chains
  132 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   75 ASP
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain H residue  566 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
C  59 GLN
E  56 ASN
H 666 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.073294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.059540 restraints weight = 49264.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.060927 restraints weight = 28629.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.061809 restraints weight = 20104.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.062342 restraints weight = 16051.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.062745 restraints weight = 13915.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9932  Z= 0.184
  Angle     :  0.634   8.823  14146  Z= 0.365
  Chirality :  0.036   0.134   1608
  Planarity :  0.004   0.030   1241
  Dihedral  : 28.476 170.931   2785
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 16.16 %
    Favored  : 79.97 %
  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 aren not related in a simple way.
  whole:  0.08 (0.31), residues: 773
  helix:  1.45 (0.28), residues: 328
  sheet: -0.65 (0.41), residues: 154
  loop : -1.11 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E   3 
 TYR   0.011   0.001   TYR H 669 
 PHE   0.020   0.002   PHE F  55 
 TRP   0.009   0.001   TRP H 659 
 HIS   0.005   0.001   HIS E 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 9932)
  covalent geometry    : angle       0.63410 (14146)
  hydrogen bonds       : bond        0.04186 (  485)
  hydrogen bonds       : angle       4.21562 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8664 (tp30) cc_final: 0.8014 (tm-30)
REVERT: C   92 GLU cc_start: 0.6476 (pm20) cc_final: 0.6274 (pm20)
REVERT: D   29 MET cc_start: 0.8081 (mtp) cc_final: 0.7151 (mtt)
REVERT: D   33 MET cc_start: 0.8681 (mpp) cc_final: 0.7177 (mpp)
REVERT: D   79 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.6839 (t70)
REVERT: E   40 GLU cc_start: 0.7435 (tp30) cc_final: 0.7042 (tp30)
REVERT: E   61 ILE cc_start: 0.8780 (mt) cc_final: 0.8548 (tt)
REVERT: F   72 MET cc_start: 0.7297 (ttm) cc_final: 0.6956 (tmm)
REVERT: G   39 PHE cc_start: 0.7468 (t80) cc_final: 0.7111 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0753
  time to fit residues: 15.5609
Evaluate side-chains
  127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain H residue  566 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN
E  56 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.071331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.057862 restraints weight = 51355.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.059219 restraints weight = 29738.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.060076 restraints weight = 20865.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.060628 restraints weight = 16637.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.060914 restraints weight = 14376.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9932  Z= 0.241
  Angle     :  0.690  13.182  14146  Z= 0.389
  Chirality :  0.039   0.171   1608
  Planarity :  0.005   0.046   1241
  Dihedral  : 28.610 170.945   2785
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 17.45 %
    Favored  : 77.06 %
  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 aren not related in a simple way.
  whole: -0.19 (0.30), residues: 773
  helix:  1.17 (0.28), residues: 328
  sheet: -0.80 (0.39), residues: 169
  loop : -1.17 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 100 
 TYR   0.016   0.001   TYR H 815 
 PHE   0.019   0.002   PHE C  49 
 TRP   0.011   0.001   TRP H 659 
 HIS   0.006   0.002   HIS E 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 9932)
  covalent geometry    : angle       0.69008 (14146)
  hydrogen bonds       : bond        0.04907 (  485)
  hydrogen bonds       : angle       4.38758 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8750 (tp30) cc_final: 0.8070 (tm-30)
REVERT: D    1 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7473 (ptm)
REVERT: D   33 MET cc_start: 0.8922 (mpp) cc_final: 0.8392 (mpp)
REVERT: D   79 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.6879 (t70)
REVERT: E   61 ILE cc_start: 0.8762 (mt) cc_final: 0.8534 (tt)
REVERT: G   31 ASN cc_start: 0.8766 (m110) cc_final: 0.8509 (p0)
REVERT: H  640 ASP cc_start: 0.8721 (p0) cc_final: 0.8420 (p0)
REVERT: H  714 ASP cc_start: 0.5351 (OUTLIER) cc_final: 0.5044 (p0)
REVERT: H  736 GLN cc_start: 0.7835 (tp40) cc_final: 0.7550 (tm-30)
REVERT: H  802 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8424 (mm)
  outliers start: 34
  outliers final: 24
  residues processed: 128
  average time/residue: 0.0744
  time to fit residues: 14.0960
Evaluate side-chains
  127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   77 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   75 ASP
Chi-restraints excluded: chain F residue   87 ASN
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  802 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0030
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    0.2980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.5190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.073456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.060109 restraints weight = 50872.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.061496 restraints weight = 29227.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.062385 restraints weight = 20337.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.062955 restraints weight = 16128.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.063303 restraints weight = 13887.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9932  Z= 0.156
  Angle     :  0.627   9.321  14146  Z= 0.358
  Chirality :  0.036   0.160   1608
  Planarity :  0.004   0.034   1241
  Dihedral  : 28.486 168.229   2785
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 18.90 %
    Favored  : 76.74 %
  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 aren not related in a simple way.
  whole:  0.17 (0.31), residues: 773
  helix:  1.50 (0.28), residues: 328
  sheet: -0.51 (0.42), residues: 163
  loop : -1.10 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 566 
 TYR   0.010   0.001   TYR F  62 
 PHE   0.017   0.001   PHE G  55 
 TRP   0.005   0.001   TRP H 659 
 HIS   0.003   0.001   HIS E 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9932)
  covalent geometry    : angle       0.62728 (14146)
  hydrogen bonds       : bond        0.03845 (  485)
  hydrogen bonds       : angle       4.07282 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8574 (tp30) cc_final: 0.7978 (tm-30)
REVERT: E   61 ILE cc_start: 0.8736 (mt) cc_final: 0.8528 (tt)
REVERT: F   99 ASP cc_start: 0.7734 (t0) cc_final: 0.7383 (m-30)
REVERT: F  106 ILE cc_start: 0.7693 (mm) cc_final: 0.7455 (tt)
REVERT: H  647 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7259 (ptt90)
REVERT: H  714 ASP cc_start: 0.5339 (OUTLIER) cc_final: 0.5081 (p0)
REVERT: H  736 GLN cc_start: 0.7769 (tp40) cc_final: 0.7490 (tm-30)
  outliers start: 27
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0821
  time to fit residues: 14.4163
Evaluate side-chains
  120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   57 ARG
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  647 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
H 803 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.070157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.056674 restraints weight = 49172.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.058065 restraints weight = 27301.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.058974 restraints weight = 18497.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.059562 restraints weight = 14293.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.059956 restraints weight = 12116.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9932  Z= 0.214
  Angle     :  0.662   9.491  14146  Z= 0.374
  Chirality :  0.037   0.149   1608
  Planarity :  0.004   0.036   1241
  Dihedral  : 28.572 170.507   2785
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.06 %
    Favored  : 76.74 %
  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 aren not related in a simple way.
  whole: -0.02 (0.31), residues: 773
  helix:  1.34 (0.28), residues: 328
  sheet: -0.78 (0.41), residues: 170
  loop : -1.07 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 100 
 TYR   0.012   0.001   TYR H 669 
 PHE   0.021   0.002   PHE F  55 
 TRP   0.009   0.001   TRP H 659 
 HIS   0.005   0.001   HIS E 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 9932)
  covalent geometry    : angle       0.66220 (14146)
  hydrogen bonds       : bond        0.04469 (  485)
  hydrogen bonds       : angle       4.25998 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8620 (tp30) cc_final: 0.8031 (tm-30)
REVERT: D   79 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.6890 (t70)
REVERT: E   61 ILE cc_start: 0.8809 (mt) cc_final: 0.8584 (tt)
REVERT: F   72 MET cc_start: 0.7952 (mmm) cc_final: 0.7510 (tpp)
REVERT: F   99 ASP cc_start: 0.7780 (t0) cc_final: 0.7457 (m-30)
REVERT: F  106 ILE cc_start: 0.7780 (mm) cc_final: 0.7520 (tt)
REVERT: G   99 ASP cc_start: 0.8546 (m-30) cc_final: 0.8066 (p0)
REVERT: H  647 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7261 (ptt90)
REVERT: H  714 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5222 (p0)
REVERT: H  736 GLN cc_start: 0.7891 (tp40) cc_final: 0.7504 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0683
  time to fit residues: 12.3834
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   57 ARG
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  647 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  775 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
G  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.070754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.057316 restraints weight = 48394.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.058714 restraints weight = 26669.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.059634 restraints weight = 18051.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.060239 restraints weight = 13913.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.060561 restraints weight = 11739.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9932  Z= 0.187
  Angle     :  0.656   9.115  14146  Z= 0.371
  Chirality :  0.036   0.142   1608
  Planarity :  0.004   0.035   1241
  Dihedral  : 28.582 168.966   2785
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 19.87 %
    Favored  : 75.44 %
  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 aren not related in a simple way.
  whole:  0.06 (0.31), residues: 773
  helix:  1.40 (0.28), residues: 328
  sheet: -0.63 (0.42), residues: 165
  loop : -1.12 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 100 
 TYR   0.015   0.001   TYR C  11 
 PHE   0.015   0.002   PHE F  55 
 TRP   0.006   0.001   TRP H 659 
 HIS   0.004   0.001   HIS F 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9932)
  covalent geometry    : angle       0.65568 (14146)
  hydrogen bonds       : bond        0.04187 (  485)
  hydrogen bonds       : angle       4.16171 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   79 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.6854 (t70)
REVERT: E   61 ILE cc_start: 0.8807 (mt) cc_final: 0.8583 (tt)
REVERT: E   72 MET cc_start: 0.7360 (ttm) cc_final: 0.7091 (ttm)
REVERT: F   72 MET cc_start: 0.7931 (mmm) cc_final: 0.7498 (tpp)
REVERT: F   99 ASP cc_start: 0.7808 (t0) cc_final: 0.7485 (m-30)
REVERT: F  106 ILE cc_start: 0.7735 (mm) cc_final: 0.7479 (tt)
REVERT: H  647 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7277 (ptt90)
REVERT: H  714 ASP cc_start: 0.5493 (OUTLIER) cc_final: 0.5187 (p0)
REVERT: H  736 GLN cc_start: 0.7894 (tp40) cc_final: 0.7514 (tm-30)
REVERT: H  802 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8439 (mm)
  outliers start: 29
  outliers final: 23
  residues processed: 122
  average time/residue: 0.0755
  time to fit residues: 13.1406
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   57 ARG
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   77 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   87 ASN
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  647 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  775 VAL
Chi-restraints excluded: chain H residue  802 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D  79 HIS
G  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.070976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.057448 restraints weight = 48103.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.058842 restraints weight = 26739.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.059749 restraints weight = 18200.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.060317 restraints weight = 14086.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.060739 restraints weight = 11930.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
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      :  0.004   0.039   9932  Z= 0.180
  Angle     :  0.664  10.612  14146  Z= 0.372
  Chirality :  0.036   0.140   1608
  Planarity :  0.004   0.035   1241
  Dihedral  : 28.569 168.205   2785
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.87 %
    Favored  : 75.61 %
  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 aren not related in a simple way.
  whole:  0.05 (0.31), residues: 773
  helix:  1.40 (0.28), residues: 328
  sheet: -0.76 (0.40), residues: 176
  loop : -1.04 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 100 
 TYR   0.011   0.001   TYR F  52 
 PHE   0.021   0.002   PHE G 111 
 TRP   0.006   0.001   TRP G  91 
 HIS   0.004   0.001   HIS F 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9932)
  covalent geometry    : angle       0.66383 (14146)
  hydrogen bonds       : bond        0.04089 (  485)
  hydrogen bonds       : angle       4.13006 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7634 (ptm) cc_final: 0.7024 (ptt)
REVERT: D   79 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7076 (t-90)
REVERT: F   72 MET cc_start: 0.7902 (mmm) cc_final: 0.7456 (tpp)
REVERT: F   99 ASP cc_start: 0.7799 (t0) cc_final: 0.7484 (m-30)
REVERT: F  106 ILE cc_start: 0.7715 (mm) cc_final: 0.7477 (tt)
REVERT: G   99 ASP cc_start: 0.8570 (m-30) cc_final: 0.8071 (p0)
REVERT: H  647 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7322 (ptt90)
REVERT: H  714 ASP cc_start: 0.5484 (OUTLIER) cc_final: 0.5190 (p0)
REVERT: H  736 GLN cc_start: 0.7879 (tp40) cc_final: 0.7519 (tm-30)
  outliers start: 28
  outliers final: 21
  residues processed: 120
  average time/residue: 0.0728
  time to fit residues: 12.7768
Evaluate side-chains
  125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   57 ARG
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  647 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0050
   chunk 62 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.4794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.072073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.058568 restraints weight = 48582.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.059962 restraints weight = 27100.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.060879 restraints weight = 18458.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.061505 restraints weight = 14291.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.061870 restraints weight = 12020.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.4725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9932  Z= 0.156
  Angle     :  0.647  10.028  14146  Z= 0.364
  Chirality :  0.036   0.169   1608
  Planarity :  0.004   0.036   1241
  Dihedral  : 28.438 166.254   2785
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 20.19 %
    Favored  : 75.44 %
  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 aren not related in a simple way.
  whole:  0.19 (0.32), residues: 773
  helix:  1.53 (0.28), residues: 329
  sheet: -0.75 (0.39), residues: 177
  loop : -0.93 (0.42), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 100 
 TYR   0.011   0.001   TYR F  52 
 PHE   0.014   0.001   PHE G 111 
 TRP   0.006   0.001   TRP G  91 
 HIS   0.013   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9932)
  covalent geometry    : angle       0.64657 (14146)
  hydrogen bonds       : bond        0.03776 (  485)
  hydrogen bonds       : angle       4.01199 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7612 (ptm) cc_final: 0.6964 (ptt)
REVERT: D   79 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6714 (t70)
REVERT: E   13 MET cc_start: 0.7656 (ppp) cc_final: 0.6933 (ttp)
REVERT: F   72 MET cc_start: 0.7864 (mmm) cc_final: 0.7455 (tpp)
REVERT: F   99 ASP cc_start: 0.7769 (t0) cc_final: 0.7486 (m-30)
REVERT: G   99 ASP cc_start: 0.8501 (m-30) cc_final: 0.8047 (p0)
REVERT: H  647 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7295 (ptt90)
REVERT: H  714 ASP cc_start: 0.5450 (OUTLIER) cc_final: 0.5198 (p0)
REVERT: H  736 GLN cc_start: 0.7893 (tp40) cc_final: 0.7548 (tm-30)
  outliers start: 27
  outliers final: 19
  residues processed: 121
  average time/residue: 0.0842
  time to fit residues: 14.5602
Evaluate side-chains
  121 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   57 ARG
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   10 THR
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain H residue  595 GLU
Chi-restraints excluded: chain H residue  647 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 92 optimal weight:   20.0000
   chunk 48 optimal weight:    0.0040
   chunk 67 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0470
   chunk 73 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 63 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4890

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

Flipped N/Q/H residues before XYZ refinement:
D  79 HIS
G  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.072304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.058866 restraints weight = 48710.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.060242 restraints weight = 27106.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.061155 restraints weight = 18491.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.061750 restraints weight = 14372.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.062114 restraints weight = 12147.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9932  Z= 0.156
  Angle     :  0.659  10.579  14146  Z= 0.366
  Chirality :  0.037   0.397   1608
  Planarity :  0.004   0.031   1241
  Dihedral  : 28.334 166.152   2785
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.81 %
    Favored  : 74.64 %
  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 aren not related in a simple way.
  whole:  0.22 (0.32), residues: 773
  helix:  1.55 (0.28), residues: 329
  sheet: -0.67 (0.40), residues: 175
  loop : -0.97 (0.41), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 100 
 TYR   0.011   0.001   TYR F  52 
 PHE   0.031   0.002   PHE G 111 
 TRP   0.006   0.001   TRP G  91 
 HIS   0.002   0.001   HIS E 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9932)
  covalent geometry    : angle       0.65879 (14146)
  hydrogen bonds       : bond        0.03772 (  485)
  hydrogen bonds       : angle       3.99701 ( 1230)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7602 (ptm) cc_final: 0.7042 (ptt)
REVERT: D   79 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6892 (t-90)
REVERT: E   13 MET cc_start: 0.7492 (ppp) cc_final: 0.7158 (tmm)
REVERT: E   74 LEU cc_start: 0.7599 (tp) cc_final: 0.7262 (tp)
REVERT: F   72 MET cc_start: 0.7838 (mmm) cc_final: 0.7416 (tpp)
REVERT: F   99 ASP cc_start: 0.7755 (t0) cc_final: 0.7448 (m-30)
REVERT: G   82 LEU cc_start: 0.9231 (tp) cc_final: 0.8896 (pp)
REVERT: G   99 ASP cc_start: 0.8510 (m-30) cc_final: 0.8051 (p0)
REVERT: H  647 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7302 (ptt90)
REVERT: H  714 ASP cc_start: 0.5427 (OUTLIER) cc_final: 0.5201 (p0)
REVERT: H  736 GLN cc_start: 0.7877 (tp40) cc_final: 0.7539 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 122
  average time/residue: 0.0807
  time to fit residues: 14.0767
Evaluate side-chains
  121 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   57 ARG
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   10 THR
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   70 LEU
Chi-restraints excluded: chain H residue  647 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  714 ASP
Chi-restraints excluded: chain H residue  735 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
E  50 HIS
E  56 ASN
E  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.069183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.055703 restraints weight = 49151.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.057050 restraints weight = 27886.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.057931 restraints weight = 19165.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.058518 restraints weight = 14940.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.058885 restraints weight = 12632.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9932  Z= 0.262
  Angle     :  0.734   9.532  14146  Z= 0.409
  Chirality :  0.040   0.293   1608
  Planarity :  0.004   0.034   1241
  Dihedral  : 28.599 169.635   2785
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.65 %
    Favored  : 74.15 %
  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 aren not related in a simple way.
  whole: -0.25 (0.31), residues: 773
  helix:  1.06 (0.27), residues: 325
  sheet: -0.97 (0.39), residues: 184
  loop : -0.95 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 100 
 TYR   0.017   0.002   TYR H 669 
 PHE   0.026   0.002   PHE D  80 
 TRP   0.010   0.002   TRP H 659 
 HIS   0.006   0.002   HIS F 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 9932)
  covalent geometry    : angle       0.73356 (14146)
  hydrogen bonds       : bond        0.05246 (  485)
  hydrogen bonds       : angle       4.49497 ( 1230)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1640.01 seconds
wall clock time: 28 minutes 55.50 seconds (1735.50 seconds total)