Starting phenix.real_space_refine
on Tue Jul 29 22:52:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f11_50121/07_2025/9f11_50121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f11_50121/07_2025/9f11_50121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_2025/9f11_50121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_2025/9f11_50121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_2025/9f11_50121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_2025/9f11_50121.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     181      5.49       5
     Mg      1      5.21       5
     S      32      5.16       5
     C    6911      2.51       5
     N    2172      2.21       5
     O    2653      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11950
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1982
          Classifications: {'DNA': 96}
          Link IDs: {'rna3p': 95}
    Chain: "B"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1739
          Classifications: {'DNA': 85}
          Link IDs: {'rna3p': 84}
    Chain: "C"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 764
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "D"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 749
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 917
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 3, 'TRANS': 109}
    Chain: "F"
      Number of atoms: 958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 958
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 787
          Classifications: {'peptide': 104}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 3, 'TRANS': 100}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 78
          Planarities with less than four sites: {'PHE:plan': 4, 'TYR:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "H"
      Number of atoms: 4053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4053
          Classifications: {'peptide': 543}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 21, 'TRANS': 521}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 171
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 107
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 10.72, per 1000 atoms: 0.90
  Number of scatterers: 11950
  At special positions: 0
  Unit cell: (94.05, 130.35, 181.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P     181     15.00
     Mg      1     11.99
     O    2653      8.00
     N    2172      7.00
     C    6911      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: 3.14
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 13 sheets defined
      45.4% alpha, 17.5% beta
      75 base pairs and 156 stacking pairs defined.
    Time for finding SS restraints: 4.95
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 17
    Processing helix  chain 'C' and resid 19 through 40
      removed outlier: 3.574A  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: 3.513A  pdb=" N   GLU D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN D  13 " --> pdb=" O   ARG D   9 " (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 20 through 34
      removed outlier: 3.881A  pdb=" N   SER E  24 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ARG E  32 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 52
      removed outlier: 3.536A  pdb=" N   ALA E  41 " --> pdb=" O   ARG E  37 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP E  47 " --> pdb=" O   ILE E  43 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS E  50 " --> pdb=" O   LYS E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 90
    Processing helix  chain 'E' and resid 92 through 108
    Processing helix  chain 'F' and resid 20 through 34
      removed outlier: 3.750A  pdb=" N   SER F  24 " --> pdb=" O   VAL F  20 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU F  25 " --> pdb=" O   ASP F  21 " (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
      removed outlier: 3.607A  pdb=" N   ASP F 103 " --> pdb=" O   ASP F  99 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 20 through 34
      removed outlier: 4.035A  pdb=" N   SER G  24 " --> pdb=" O   VAL G  20 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LEU G  25 " --> pdb=" O   ASP G  21 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU G  26 " --> pdb=" O   VAL G  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 52
      removed outlier: 3.809A  pdb=" N   HIS G  50 " --> pdb=" O   LYS G  46 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR G  52 " --> pdb=" O   HIS G  48 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 75 through 90
    Processing helix  chain 'G' and resid 92 through 108
    Processing helix  chain 'H' and resid 11 through 15
      removed outlier: 3.676A  pdb=" N   GLY H  14 " --> pdb=" O   GLY H  11 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASN H  15 " --> pdb=" O   SER H  12 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 11 through 15'
    Processing helix  chain 'H' and resid 35 through 42
    Processing helix  chain 'H' and resid 48 through 57
    Processing helix  chain 'H' and resid 87 through 98
    Processing helix  chain 'H' and resid 99 through 101
      No H-bonds generated for 'chain 'H' and resid 99 through 101'
    Processing helix  chain 'H' and resid 102 through 118
      removed outlier: 3.757A  pdb=" N   GLN H 116 " --> pdb=" O   PHE H 112 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 184 through 192
    Processing helix  chain 'H' and resid 192 through 211
      removed outlier: 3.516A  pdb=" N   LYS H 203 " --> pdb=" O   LEU H 199 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN H 207 " --> pdb=" O   LYS H 203 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 231 through 234
    Processing helix  chain 'H' and resid 235 through 246
    Processing helix  chain 'H' and resid 251 through 262
    Processing helix  chain 'H' and resid 271 through 285
    Processing helix  chain 'H' and resid 287 through 298
      removed outlier: 3.767A  pdb=" N   TYR H 291 " --> pdb=" O   ASP H 287 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG H 292 " --> pdb=" O   ILE H 288 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP H 293 " --> pdb=" O   ARG H 289 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 576 through 594
    Processing helix  chain 'H' and resid 603 through 621
      removed outlier: 3.549A  pdb=" N   ALA H 608 " --> pdb=" O   VAL H 604 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 646 through 650
      removed outlier: 3.511A  pdb=" N   MET H 649 " --> pdb=" O   LEU H 646 " (cutoff:3.500A)
    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 798 through 808
      removed outlier: 3.509A  pdb=" N   SER H 808 " --> pdb=" O   GLY H 804 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 822 through 827
    Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46
      removed outlier: 3.679A  pdb=" N   VAL C  44 " --> pdb=" O   PHE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 45
    Processing sheet with id=AA3, first strand: chain 'D' and resid 59 through 62
    Processing sheet with id=AA4, first strand: chain 'E' and resid 13 through 19
    Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 19
    Processing sheet with id=AA6, first strand: chain 'G' and resid 14 through 19
    Processing sheet with id=AA7, first strand: chain 'H' and resid 2 through 7
      removed outlier: 4.515A  pdb=" N   GLY H  79 " --> pdb=" O   VAL H   7 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL H 161 " --> pdb=" O   ALA H 142 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   VAL H 140 " --> pdb=" O   ALA H 163 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 69 through 70
    Processing sheet with id=AA9, first strand: chain 'H' and resid 122 through 126
    Processing sheet with id=AB1, first strand: chain 'H' and resid 216 through 219
      removed outlier: 6.818A  pdb=" N   MET H 223 " --> pdb=" O   VAL H 218 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 568 through 572
      removed outlier: 6.744A  pdb=" N   VAL H 788 " --> pdb=" O   ARG H 813 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR H 815 " --> pdb=" O   VAL H 788 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ALA H 790 " --> pdb=" O   TYR H 815 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL H 598 " --> pdb=" O   PHE H 789 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   SER H 791 " --> pdb=" O   VAL H 598 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   GLN H 600 " --> pdb=" O   SER H 791 " (cutoff:3.500A)
      removed outlier: 9.295A  pdb=" N   GLU H 776 " --> pdb=" O   SER H 597 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA H 599 " --> pdb=" O   GLU H 776 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 629 through 636
      removed outlier: 6.660A  pdb=" N   THR H 682 " --> pdb=" O   ASP H 672 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   VAL H 674 " --> pdb=" O   SER H 680 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER H 680 " --> pdb=" O   VAL H 674 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 755 through 759
      removed outlier: 6.647A  pdb=" N   VAL H 748 " --> pdb=" O   VAL H 737 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   VAL H 737 " --> pdb=" O   VAL H 748 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      169 hydrogen bonds
      334 hydrogen bond angles
      0 basepair planarities
      75 basepair parallelities
      156 stacking parallelities
  Total time for adding SS restraints: 5.23

  Time building geometry restraints manager: 3.73 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: 2588
        1.33 -     1.45: 3397
        1.45 -     1.57: 6124
        1.57 -     1.69: 360
        1.69 -     1.81: 61
  Bond restraints: 12530
  Sorted by residual:
  bond pdb=" P    DT A   8 "
       pdb=" OP2  DT A   8 "
    ideal  model  delta    sigma   weight residual
    1.480  1.519 -0.039 2.00e-02 2.50e+03 3.90e+00
  bond pdb=" P    DT B  31 "
       pdb=" OP2  DT B  31 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.57e+00
  bond pdb=" N   LEU H 802 "
       pdb=" CA  LEU H 802 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.21e-02 6.83e+03 3.23e+00
  bond pdb=" P    DT A   8 "
       pdb=" OP1  DT A   8 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.14e+00
  bond pdb=" P    DG A   7 "
       pdb=" OP1  DG A   7 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.11e+00
  ... (remaining 12525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 17317
        2.14 -     4.29: 348
        4.29 -     6.43: 28
        6.43 -     8.57: 7
        8.57 -    10.71: 4
  Bond angle restraints: 17704
  Sorted by residual:
  angle pdb=" O3'  DT A   8 "
        pdb=" C3'  DT A   8 "
        pdb=" C2'  DT A   8 "
      ideal   model   delta    sigma   weight residual
     111.50  102.94    8.56 1.50e+00 4.44e-01 3.26e+01
  angle pdb=" C   HIS H 168 "
        pdb=" CA  HIS H 168 "
        pdb=" CB  HIS H 168 "
      ideal   model   delta    sigma   weight residual
     116.54  111.14    5.40 1.15e+00 7.56e-01 2.21e+01
  angle pdb=" O3'  DG A   9 "
        pdb=" P    DT A   8 "
        pdb=" O5'  DT A   8 "
      ideal   model   delta    sigma   weight residual
     104.00   96.97    7.03 1.50e+00 4.44e-01 2.19e+01
  angle pdb=" C3'  DG A   9 "
        pdb=" O3'  DG A   9 "
        pdb=" P    DT A   8 "
      ideal   model   delta    sigma   weight residual
     120.20  127.16   -6.96 1.50e+00 4.44e-01 2.15e+01
  angle pdb=" O3'  DT A   8 "
        pdb=" P    DG A   7 "
        pdb=" O5'  DG A   7 "
      ideal   model   delta    sigma   weight residual
     104.00   97.25    6.75 1.50e+00 4.44e-01 2.03e+01
  ... (remaining 17699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.09: 6342
       35.09 -    70.18: 828
       70.18 -   105.27: 12
      105.27 -   140.36: 1
      140.36 -   175.45: 3
  Dihedral angle restraints: 7186
    sinusoidal: 4122
      harmonic: 3064
  Sorted by residual:
  dihedral pdb=" CA  THR F   6 "
           pdb=" C   THR F   6 "
           pdb=" N   ARG F   7 "
           pdb=" CA  ARG F   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.54  -23.46     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  PHE E   4 "
           pdb=" C   PHE E   4 "
           pdb=" N   GLY E   5 "
           pdb=" CA  GLY E   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.66  -22.34     0      5.00e+00 4.00e-02 2.00e+01
  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
     220.00   44.55  175.45     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7183 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1954
       0.111 -    0.222: 24
       0.222 -    0.333: 0
       0.333 -    0.444: 2
       0.444 -    0.555: 8
  Chirality restraints: 1988
  Sorted by residual:
  chirality pdb=" P    DA B  83 "
            pdb=" OP1  DA B  83 "
            pdb=" OP2  DA B  83 "
            pdb=" O5'  DA B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.90   -0.56 2.00e-01 2.50e+01 7.70e+00
  chirality pdb=" P    DT A   8 "
            pdb=" OP1  DT A   8 "
            pdb=" OP2  DT A   8 "
            pdb=" O5'  DT A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.89   -0.55 2.00e-01 2.50e+01 7.53e+00
  chirality pdb=" P    DG A   7 "
            pdb=" OP1  DG A   7 "
            pdb=" OP2  DG A   7 "
            pdb=" O5'  DG A   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.88   -0.54 2.00e-01 2.50e+01 7.24e+00
  ... (remaining 1985 not shown)

  Planarity restraints: 1651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  46 "   -0.026 2.00e-02 2.50e+03   1.23e-02 3.79e+00
        pdb=" N1   DT A  46 "    0.025 2.00e-02 2.50e+03
        pdb=" C2   DT A  46 "    0.000 2.00e-02 2.50e+03
        pdb=" O2   DT A  46 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DT A  46 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4   DT A  46 "   -0.005 2.00e-02 2.50e+03
        pdb=" O4   DT A  46 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DT A  46 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT A  46 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DT A  46 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA A  21 "    0.024 2.00e-02 2.50e+03   1.07e-02 3.16e+00
        pdb=" N9   DA A  21 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8   DA A  21 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7   DA A  21 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA A  21 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA A  21 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA A  21 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA A  21 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DA A  21 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA A  21 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA A  21 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  13 "    0.022 2.00e-02 2.50e+03   1.09e-02 2.98e+00
        pdb=" N1   DT A  13 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2   DT A  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DT A  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DT A  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DT A  13 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT A  13 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DT A  13 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT A  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DT A  13 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1648 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 36
        2.43 -     3.05: 7148
        3.05 -     3.67: 19354
        3.67 -     4.28: 29150
        4.28 -     4.90: 43934
  Nonbonded interactions: 99622
  Sorted by model distance:
  nonbonded pdb=" OP1  DG A  -1 "
            pdb="MG    MG H1801 "
     model   vdw
     1.813 2.170
  nonbonded pdb=" NE2 HIS H 157 "
            pdb="MG    MG H1801 "
     model   vdw
     1.890 2.250
  nonbonded pdb=" ND1 HIS H 146 "
            pdb="MG    MG H1801 "
     model   vdw
     1.962 2.250
  nonbonded pdb=" OG  SER E  30 "
            pdb=" O   ARG E  35 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OE2 GLU H 209 "
            pdb=" OG1 THR H 215 "
     model   vdw
     2.213 3.040
  ... (remaining 99617 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 53 or (resid 54 through 55 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ 
name N or name CA or name C or name O or name CB )) or (resid 62 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 63 or (resid 64 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 65 through 68 or (resid 69  \ 
and (name N or name CA or name C or name O or name CB )) or resid 70 through 72  \ 
or (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 
4 through 95 or (resid 96 through 98 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 99 through 106 or (resid 107 through 108 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 109 through 110 or (resid 111  \ 
and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 
3))
  selection = (chain 'F' 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 53 or (resid 54 through 55 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ 
name N or name CA or name C or name O or name CB )) or (resid 62 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 63 through 68 or (resid 69 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 70 through 72 or \ 
 (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74  \ 
through 95 or (resid 96 through 98 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 99 through 106 or (resid 107 through 108 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 109 through 110 or (resid 111 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 112 through 113) \ 
)
  selection = (chain 'G' and resid 12 through 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:             9.470
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     37.960
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
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   0.050  12530  Z= 0.216
  Angle     :  0.682  10.715  17704  Z= 0.393
  Chirality :  0.051   0.555   1988
  Planarity :  0.004   0.036   1651
  Dihedral  : 23.271 175.445   5198
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.20 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.25), residues: 1039
  helix:  0.60 (0.24), residues: 451
  sheet: -0.55 (0.36), residues: 202
  loop : -0.42 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 224 
 HIS   0.004   0.001   HIS H 106 
 PHE   0.010   0.001   PHE E  55 
 TYR   0.011   0.001   TYR H 669 
 ARG   0.010   0.000   ARG C  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17539 (  593)
  hydrogen bonds       : angle       6.88021 ( 1561)
  covalent geometry    : bond        0.00467 (12530)
  covalent geometry    : angle       0.68186 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 270
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   50 SER cc_start: 0.8943 (p) cc_final: 0.8717 (m)
REVERT: D   68 ASP cc_start: 0.7807 (m-30) cc_final: 0.7591 (t70)
REVERT: F   43 ILE cc_start: 0.8981 (mt) cc_final: 0.8711 (mt)
REVERT: G   14 VAL cc_start: 0.8569 (t) cc_final: 0.8366 (m)
REVERT: G   31 ASN cc_start: 0.8033 (m-40) cc_final: 0.7756 (m-40)
REVERT: G   39 PHE cc_start: 0.8321 (t80) cc_final: 0.7757 (t80)
REVERT: G  102 ILE cc_start: 0.9156 (mt) cc_final: 0.8853 (tp)
REVERT: H    1 MET cc_start: 0.7250 (tpt) cc_final: 0.6940 (tpp)
REVERT: H    2 MET cc_start: 0.7662 (ttt) cc_final: 0.7411 (ttp)
REVERT: H   95 MET cc_start: 0.6253 (mmt) cc_final: 0.5945 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 272
  average time/residue: 0.2815
  time to fit residues: 103.6305
Evaluate side-chains
  119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  158 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 70 optimal weight:   10.0000
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
D  13 GLN
H   6 GLN
H 155 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.080138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.060089 restraints weight = 48323.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.061589 restraints weight = 26185.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062533 restraints weight = 17997.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12530  Z= 0.210
  Angle     :  0.648   6.898  17704  Z= 0.371
  Chirality :  0.038   0.154   1988
  Planarity :  0.005   0.046   1651
  Dihedral  : 27.766 172.566   3232
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.53 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1039
  helix:  1.10 (0.23), residues: 463
  sheet: -0.55 (0.38), residues: 188
  loop : -0.57 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 774 
 HIS   0.005   0.001   HIS H 221 
 PHE   0.020   0.002   PHE C  13 
 TYR   0.016   0.002   TYR G  52 
 ARG   0.007   0.001   ARG H 810 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  593)
  hydrogen bonds       : angle       4.73629 ( 1561)
  covalent geometry    : bond        0.00461 (12530)
  covalent geometry    : angle       0.64821 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8094 (m-30) cc_final: 0.7566 (t70)
REVERT: F   39 PHE cc_start: 0.8921 (t80) cc_final: 0.8647 (t80)
REVERT: F   77 GLU cc_start: 0.7227 (pp20) cc_final: 0.6686 (tm-30)
REVERT: G   23 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7453 (mp0)
REVERT: G   31 ASN cc_start: 0.8213 (m-40) cc_final: 0.7782 (m-40)
REVERT: H    1 MET cc_start: 0.7069 (tpt) cc_final: 0.6740 (tpt)
REVERT: H    2 MET cc_start: 0.7511 (ttt) cc_final: 0.7003 (ttp)
REVERT: H   95 MET cc_start: 0.6299 (mmt) cc_final: 0.5617 (mtt)
REVERT: H  190 TYR cc_start: 0.8300 (m-80) cc_final: 0.7850 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 146
  average time/residue: 0.2731
  time to fit residues: 59.1578
Evaluate side-chains
  116 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   56 ASN
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  693 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 115 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0670
   chunk 110 optimal weight:    0.8980
   chunk 88 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
G 113 ASN
H   6 GLN
H 612 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.080916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.061062 restraints weight = 49307.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.062609 restraints weight = 26586.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063530 restraints weight = 18121.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12530  Z= 0.159
  Angle     :  0.579   5.952  17704  Z= 0.335
  Chirality :  0.035   0.145   1988
  Planarity :  0.004   0.048   1651
  Dihedral  : 27.509 175.929   3232
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 12.65 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1039
  helix:  1.37 (0.24), residues: 464
  sheet: -0.56 (0.36), residues: 198
  loop : -0.37 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 277 
 HIS   0.003   0.001   HIS H 679 
 PHE   0.012   0.001   PHE C  13 
 TYR   0.018   0.001   TYR G  52 
 ARG   0.005   0.000   ARG H 810 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  593)
  hydrogen bonds       : angle       4.26782 ( 1561)
  covalent geometry    : bond        0.00344 (12530)
  covalent geometry    : angle       0.57861 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8111 (m-30) cc_final: 0.7653 (t70)
REVERT: G   31 ASN cc_start: 0.8237 (m-40) cc_final: 0.7880 (m-40)
REVERT: G   37 ARG cc_start: 0.8071 (ptp-170) cc_final: 0.7783 (ptt180)
REVERT: H    1 MET cc_start: 0.7281 (tpt) cc_final: 0.6981 (tpt)
REVERT: H    2 MET cc_start: 0.7515 (ttt) cc_final: 0.7156 (tmm)
REVERT: H   95 MET cc_start: 0.6092 (mmt) cc_final: 0.5304 (mtp)
REVERT: H  190 TYR cc_start: 0.8208 (m-80) cc_final: 0.7772 (m-80)
  outliers start: 24
  outliers final: 21
  residues processed: 139
  average time/residue: 0.3204
  time to fit residues: 68.1050
Evaluate side-chains
  126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 2.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   56 ASN
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain F residue   46 LYS
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   27 ILE
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 114 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    0.1980
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
H   6 GLN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.080939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.062794 restraints weight = 48261.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.063257 restraints weight = 27491.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.063478 restraints weight = 20105.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12530  Z= 0.154
  Angle     :  0.564   5.780  17704  Z= 0.327
  Chirality :  0.035   0.136   1988
  Planarity :  0.004   0.043   1651
  Dihedral  : 27.383 175.251   3232
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.34 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1039
  helix:  1.47 (0.24), residues: 467
  sheet: -0.55 (0.36), residues: 199
  loop : -0.38 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 679 
 PHE   0.014   0.001   PHE C  13 
 TYR   0.024   0.001   TYR G  52 
 ARG   0.004   0.000   ARG H 810 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03428 (  593)
  hydrogen bonds       : angle       4.12223 ( 1561)
  covalent geometry    : bond        0.00333 (12530)
  covalent geometry    : angle       0.56391 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8160 (m-30) cc_final: 0.7636 (t70)
REVERT: G   31 ASN cc_start: 0.8210 (m-40) cc_final: 0.7846 (m-40)
REVERT: G   37 ARG cc_start: 0.8140 (ptp-170) cc_final: 0.7714 (ptt180)
REVERT: H    1 MET cc_start: 0.7285 (tpt) cc_final: 0.6940 (tpt)
REVERT: H   95 MET cc_start: 0.6011 (mmt) cc_final: 0.5261 (mtp)
REVERT: H  190 TYR cc_start: 0.8056 (m-80) cc_final: 0.7724 (m-80)
REVERT: H  662 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8442 (mp0)
  outliers start: 26
  outliers final: 20
  residues processed: 127
  average time/residue: 0.2189
  time to fit residues: 42.3459
Evaluate side-chains
  122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 LYS
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  662 GLU
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 42 optimal weight:    0.2980
   chunk 90 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 70 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.080629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.060927 restraints weight = 48283.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062440 restraints weight = 26153.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.063394 restraints weight = 17898.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12530  Z= 0.163
  Angle     :  0.563   5.450  17704  Z= 0.327
  Chirality :  0.035   0.134   1988
  Planarity :  0.004   0.040   1651
  Dihedral  : 27.344 175.460   3232
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.46 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1039
  helix:  1.53 (0.24), residues: 467
  sheet: -0.34 (0.37), residues: 192
  loop : -0.41 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 679 
 PHE   0.022   0.002   PHE F  39 
 TYR   0.026   0.002   TYR G  52 
 ARG   0.004   0.000   ARG H 810 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  593)
  hydrogen bonds       : angle       4.08093 ( 1561)
  covalent geometry    : bond        0.00356 (12530)
  covalent geometry    : angle       0.56324 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8098 (m-30) cc_final: 0.7675 (t70)
REVERT: E   43 ILE cc_start: 0.9458 (tp) cc_final: 0.9254 (mm)
REVERT: E   95 ASP cc_start: 0.7846 (m-30) cc_final: 0.7176 (m-30)
REVERT: F   77 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7825 (tm-30)
REVERT: G   31 ASN cc_start: 0.8303 (m-40) cc_final: 0.7929 (m-40)
REVERT: G   37 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.7756 (ptt180)
REVERT: H    1 MET cc_start: 0.7181 (tpt) cc_final: 0.6930 (tpt)
REVERT: H    2 MET cc_start: 0.7159 (ttp) cc_final: 0.6866 (tmm)
REVERT: H  190 TYR cc_start: 0.8116 (m-80) cc_final: 0.7840 (m-80)
REVERT: H  278 MET cc_start: 0.7961 (mmp) cc_final: 0.7721 (mmm)
REVERT: H  596 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5707 (tm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 126
  average time/residue: 0.2234
  time to fit residues: 43.2339
Evaluate side-chains
  125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   56 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain F residue   77 GLU
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  590 SER
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.080414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.060642 restraints weight = 48866.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.062146 restraints weight = 26474.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063080 restraints weight = 18072.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12530  Z= 0.169
  Angle     :  0.566   5.353  17704  Z= 0.329
  Chirality :  0.035   0.157   1988
  Planarity :  0.004   0.038   1651
  Dihedral  : 27.318 175.445   3232
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 13.69 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.26), residues: 1039
  helix:  1.61 (0.24), residues: 467
  sheet: -0.50 (0.37), residues: 198
  loop : -0.36 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 159 
 PHE   0.025   0.002   PHE F  39 
 TYR   0.030   0.001   TYR G  52 
 ARG   0.004   0.000   ARG C  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03487 (  593)
  hydrogen bonds       : angle       4.06202 ( 1561)
  covalent geometry    : bond        0.00370 (12530)
  covalent geometry    : angle       0.56644 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 1.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   29 MET cc_start: 0.7576 (mtt) cc_final: 0.7375 (mtt)
REVERT: D   68 ASP cc_start: 0.8152 (m-30) cc_final: 0.7732 (t70)
REVERT: E   13 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6876 (ttp)
REVERT: E   43 ILE cc_start: 0.9453 (tp) cc_final: 0.9234 (mm)
REVERT: E   95 ASP cc_start: 0.7858 (m-30) cc_final: 0.7196 (m-30)
REVERT: G   31 ASN cc_start: 0.8314 (m-40) cc_final: 0.7935 (m-40)
REVERT: G   37 ARG cc_start: 0.8188 (ptp-170) cc_final: 0.7819 (ptt180)
REVERT: H    1 MET cc_start: 0.7285 (tpt) cc_final: 0.6997 (tpt)
REVERT: H    2 MET cc_start: 0.7399 (ttp) cc_final: 0.6901 (tmm)
REVERT: H  190 TYR cc_start: 0.8143 (m-80) cc_final: 0.7880 (m-80)
REVERT: H  278 MET cc_start: 0.7977 (mmp) cc_final: 0.7758 (mmm)
REVERT: H  596 GLU cc_start: 0.6047 (tm-30) cc_final: 0.5669 (tm-30)
  outliers start: 32
  outliers final: 24
  residues processed: 125
  average time/residue: 0.2806
  time to fit residues: 53.6447
Evaluate side-chains
  120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  229 VAL
Chi-restraints excluded: chain H residue  284 THR
Chi-restraints excluded: chain H residue  590 SER
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 63 optimal weight:    0.0870
   chunk 52 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 117 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
F  50 HIS
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.080980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.061349 restraints weight = 49431.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062817 restraints weight = 27430.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.063749 restraints weight = 18930.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12530  Z= 0.150
  Angle     :  0.557   6.237  17704  Z= 0.324
  Chirality :  0.035   0.151   1988
  Planarity :  0.003   0.038   1651
  Dihedral  : 27.234 175.572   3232
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 13.57 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1039
  helix:  1.70 (0.24), residues: 467
  sheet: -0.52 (0.36), residues: 201
  loop : -0.31 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 679 
 PHE   0.012   0.001   PHE C  13 
 TYR   0.033   0.001   TYR G  52 
 ARG   0.004   0.000   ARG C  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03380 (  593)
  hydrogen bonds       : angle       3.98387 ( 1561)
  covalent geometry    : bond        0.00326 (12530)
  covalent geometry    : angle       0.55708 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 2.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8182 (m-30) cc_final: 0.7758 (t70)
REVERT: E   13 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6838 (ttp)
REVERT: E   43 ILE cc_start: 0.9454 (tp) cc_final: 0.9235 (mm)
REVERT: E   95 ASP cc_start: 0.7828 (m-30) cc_final: 0.7110 (m-30)
REVERT: G   31 ASN cc_start: 0.8380 (m-40) cc_final: 0.8001 (m-40)
REVERT: G   37 ARG cc_start: 0.8210 (ptp-170) cc_final: 0.7846 (ptt180)
REVERT: H    1 MET cc_start: 0.7302 (tpt) cc_final: 0.7072 (tpt)
REVERT: H  190 TYR cc_start: 0.8154 (m-80) cc_final: 0.7929 (m-80)
REVERT: H  278 MET cc_start: 0.8023 (mmp) cc_final: 0.7802 (mmm)
  outliers start: 28
  outliers final: 24
  residues processed: 124
  average time/residue: 0.2873
  time to fit residues: 54.7668
Evaluate side-chains
  124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 2.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   27 ILE
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   chunk 81 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0370
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
** F  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 145 ASN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.080725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.062091 restraints weight = 49580.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062704 restraints weight = 31875.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.062907 restraints weight = 22683.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12530  Z= 0.191
  Angle     :  0.582   5.907  17704  Z= 0.336
  Chirality :  0.036   0.149   1988
  Planarity :  0.004   0.037   1651
  Dihedral  : 27.375 176.137   3232
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.92 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1039
  helix:  1.64 (0.24), residues: 468
  sheet: -0.62 (0.36), residues: 203
  loop : -0.40 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 638 
 HIS   0.004   0.001   HIS F  50 
 PHE   0.030   0.002   PHE F  39 
 TYR   0.034   0.002   TYR G  52 
 ARG   0.005   0.000   ARG C  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  593)
  hydrogen bonds       : angle       4.13531 ( 1561)
  covalent geometry    : bond        0.00422 (12530)
  covalent geometry    : angle       0.58198 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7581 (t0) cc_final: 0.7372 (t0)
REVERT: D   68 ASP cc_start: 0.8225 (m-30) cc_final: 0.7782 (t70)
REVERT: E   95 ASP cc_start: 0.7975 (m-30) cc_final: 0.7378 (m-30)
REVERT: G   31 ASN cc_start: 0.8193 (m-40) cc_final: 0.7824 (m-40)
REVERT: G   37 ARG cc_start: 0.8154 (ptp-170) cc_final: 0.7798 (ptt180)
  outliers start: 31
  outliers final: 27
  residues processed: 122
  average time/residue: 0.2322
  time to fit residues: 44.6198
Evaluate side-chains
  125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  229 VAL
Chi-restraints excluded: chain H residue  590 SER
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 93 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
** F  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 108 GLN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.081158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.062695 restraints weight = 49294.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.063157 restraints weight = 31742.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063461 restraints weight = 21619.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12530  Z= 0.169
  Angle     :  0.581   6.952  17704  Z= 0.335
  Chirality :  0.036   0.146   1988
  Planarity :  0.004   0.035   1651
  Dihedral  : 27.349 176.104   3232
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.73 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.26), residues: 1039
  helix:  1.62 (0.24), residues: 468
  sheet: -0.60 (0.36), residues: 201
  loop : -0.38 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 638 
 HIS   0.005   0.001   HIS F  50 
 PHE   0.034   0.002   PHE F  39 
 TYR   0.034   0.002   TYR G  52 
 ARG   0.004   0.000   ARG C  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 (  593)
  hydrogen bonds       : angle       4.10748 ( 1561)
  covalent geometry    : bond        0.00370 (12530)
  covalent geometry    : angle       0.58117 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7682 (t0) cc_final: 0.7452 (t0)
REVERT: D   68 ASP cc_start: 0.8246 (m-30) cc_final: 0.7802 (t70)
REVERT: E   95 ASP cc_start: 0.7969 (m-30) cc_final: 0.7312 (m-30)
REVERT: G   31 ASN cc_start: 0.8274 (m-40) cc_final: 0.7922 (m-40)
REVERT: G   37 ARG cc_start: 0.8207 (ptp-170) cc_final: 0.7837 (ptt180)
REVERT: H    1 MET cc_start: 0.6408 (tpt) cc_final: 0.6167 (tpt)
  outliers start: 28
  outliers final: 26
  residues processed: 121
  average time/residue: 0.2027
  time to fit residues: 37.7782
Evaluate side-chains
  123 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.081137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062735 restraints weight = 49020.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.063048 restraints weight = 32134.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063166 restraints weight = 21782.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12530  Z= 0.169
  Angle     :  0.582   7.098  17704  Z= 0.336
  Chirality :  0.036   0.151   1988
  Planarity :  0.004   0.035   1651
  Dihedral  : 27.357 176.123   3232
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.62 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1039
  helix:  1.61 (0.23), residues: 469
  sheet: -0.60 (0.37), residues: 201
  loop : -0.38 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 638 
 HIS   0.005   0.001   HIS F  50 
 PHE   0.038   0.002   PHE F  39 
 TYR   0.038   0.002   TYR G  52 
 ARG   0.004   0.000   ARG C  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  593)
  hydrogen bonds       : angle       4.10550 ( 1561)
  covalent geometry    : bond        0.00371 (12530)
  covalent geometry    : angle       0.58174 (17704)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7708 (t0) cc_final: 0.7486 (t0)
REVERT: D   68 ASP cc_start: 0.8240 (m-30) cc_final: 0.7825 (t70)
REVERT: E   95 ASP cc_start: 0.7937 (m-30) cc_final: 0.7312 (m-30)
REVERT: G   31 ASN cc_start: 0.8298 (m-40) cc_final: 0.7926 (m-40)
REVERT: G   37 ARG cc_start: 0.8209 (ptp-170) cc_final: 0.7838 (ptt180)
  outliers start: 28
  outliers final: 25
  residues processed: 116
  average time/residue: 0.2740
  time to fit residues: 49.3582
Evaluate side-chains
  121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   65 SER
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue   72 MET
Chi-restraints excluded: chain G residue  114 SER
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   32 ARG
Chi-restraints excluded: chain H residue   55 LEU
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  626 LEU
Chi-restraints excluded: chain H residue  629 VAL
Chi-restraints excluded: chain H residue  649 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  821 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9980
   chunk 120 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
** F  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 803 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.081056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.062652 restraints weight = 48757.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.063168 restraints weight = 31253.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063407 restraints weight = 21278.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12530  Z= 0.171
  Angle     :  0.585   6.999  17704  Z= 0.337
  Chirality :  0.036   0.152   1988
  Planarity :  0.004   0.036   1651
  Dihedral  : 27.367 176.192   3232
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.73 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1039
  helix:  1.63 (0.24), residues: 468
  sheet: -0.63 (0.37), residues: 201
  loop : -0.39 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 638 
 HIS   0.004   0.001   HIS F  50 
 PHE   0.038   0.002   PHE F  39 
 TYR   0.036   0.001   TYR G  52 
 ARG   0.005   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  593)
  hydrogen bonds       : angle       4.10015 ( 1561)
  covalent geometry    : bond        0.00375 (12530)
  covalent geometry    : angle       0.58491 (17704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5926.03 seconds
wall clock time: 110 minutes 41.18 seconds (6641.18 seconds total)