Starting phenix.real_space_refine
on Wed Sep 17 22:19:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f11_50121/09_2025/9f11_50121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f11_50121/09_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_50121/09_2025/9f11_50121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f11_50121/09_2025/9f11_50121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f11_50121/09_2025/9f11_50121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f11_50121/09_2025/9f11_50121.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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, 'ARG:plan': 3, 'TYR:plan': 2, '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: {'TYR:plan': 2, 'ARG:plan': 8, 'ASP:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 4}
          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: 2.87, per 1000 atoms: 0.24
  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: 0.89
  Conformation dependent library (CDL) restraints added in 514.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 1.69
  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: 2.41

  Time building geometry restraints manager: 1.24 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.950
  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:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.930
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (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
 ARG   0.010   0.000   ARG C  63 
 TYR   0.011   0.001   TYR H 669 
 PHE   0.010   0.001   PHE E  55 
 TRP   0.006   0.001   TRP H 224 
 HIS   0.004   0.001   HIS H 106 

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

*********************** 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  : 0.381 
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: 0.1314
  time to fit residues: 48.6491
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  : 0.398 
-------------------------------------------------------------------------------
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 108 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.3980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.081048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.061137 restraints weight = 48139.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.062673 restraints weight = 25803.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.063643 restraints weight = 17593.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.064264 restraints weight = 13907.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.064591 restraints weight = 12030.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12530  Z= 0.176
  Angle     :  0.630   6.877  17704  Z= 0.361
  Chirality :  0.037   0.157   1988
  Planarity :  0.004   0.045   1651
  Dihedral  : 27.652 171.658   3232
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.30 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.25), residues: 1039
  helix:  1.21 (0.24), residues: 463
  sheet: -0.47 (0.38), residues: 188
  loop : -0.51 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H 810 
 TYR   0.015   0.002   TYR G  52 
 PHE   0.015   0.002   PHE F  55 
 TRP   0.006   0.001   TRP H 774 
 HIS   0.006   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12530)
  covalent geometry    : angle       0.63002 (17704)
  hydrogen bonds       : bond        0.04014 (  593)
  hydrogen bonds       : angle       4.62604 ( 1561)

*********************** 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
  158 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8031 (m-30) cc_final: 0.7559 (t70)
REVERT: F   39 PHE cc_start: 0.8902 (t80) cc_final: 0.8673 (t80)
REVERT: G   23 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7500 (mp0)
REVERT: G   31 ASN cc_start: 0.8221 (m-40) cc_final: 0.7809 (m-40)
REVERT: G   42 VAL cc_start: 0.8653 (t) cc_final: 0.8441 (t)
REVERT: G  102 ILE cc_start: 0.9263 (mt) cc_final: 0.8991 (tp)
REVERT: H    1 MET cc_start: 0.7126 (tpt) cc_final: 0.6835 (tpt)
REVERT: H    2 MET cc_start: 0.7441 (ttt) cc_final: 0.6625 (tmm)
REVERT: H    4 ILE cc_start: 0.8253 (mp) cc_final: 0.7947 (mp)
REVERT: H   95 MET cc_start: 0.6515 (mmt) cc_final: 0.5887 (mtt)
REVERT: H  190 TYR cc_start: 0.8277 (m-80) cc_final: 0.7833 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 152
  average time/residue: 0.1049
  time to fit residues: 23.2677
Evaluate side-chains
  120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
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 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 9 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 106 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 111 optimal weight:    0.3980
   chunk 60 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
G 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.080996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.061153 restraints weight = 48759.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.062689 restraints weight = 26342.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063670 restraints weight = 17978.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.064320 restraints weight = 14174.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.064735 restraints weight = 12194.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12530  Z= 0.162
  Angle     :  0.581   5.495  17704  Z= 0.336
  Chirality :  0.036   0.136   1988
  Planarity :  0.004   0.048   1651
  Dihedral  : 27.510 175.838   3232
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.41 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1039
  helix:  1.39 (0.24), residues: 464
  sheet: -0.45 (0.36), residues: 198
  loop : -0.40 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 810 
 TYR   0.015   0.001   TYR G  52 
 PHE   0.014   0.001   PHE C  13 
 TRP   0.005   0.001   TRP H 638 
 HIS   0.006   0.001   HIS G 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12530)
  covalent geometry    : angle       0.58147 (17704)
  hydrogen bonds       : bond        0.03630 (  593)
  hydrogen bonds       : angle       4.26981 ( 1561)

*********************** 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
  142 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7614 (t0) cc_final: 0.7131 (m-40)
REVERT: D   68 ASP cc_start: 0.8025 (m-30) cc_final: 0.7650 (t70)
REVERT: G   31 ASN cc_start: 0.8277 (m-40) cc_final: 0.7894 (m-40)
REVERT: H    1 MET cc_start: 0.7111 (tpt) cc_final: 0.6810 (tpt)
REVERT: H    2 MET cc_start: 0.7507 (ttt) cc_final: 0.6954 (ttp)
REVERT: H   95 MET cc_start: 0.6138 (mmt) cc_final: 0.5447 (mtt)
REVERT: H  190 TYR cc_start: 0.8343 (m-80) cc_final: 0.7920 (m-80)
  outliers start: 23
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0903
  time to fit residues: 18.5789
Evaluate side-chains
  121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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   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   30 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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 118 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
** 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 = 0.3776 r_free = 0.3776 target = 0.080578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.060729 restraints weight = 48863.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.062276 restraints weight = 26485.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.063268 restraints weight = 18006.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.063865 restraints weight = 14178.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.064256 restraints weight = 12264.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3650

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= 0.169
  Angle     :  0.573   5.932  17704  Z= 0.332
  Chirality :  0.036   0.152   1988
  Planarity :  0.004   0.045   1651
  Dihedral  : 27.385 175.038   3232
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.46 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1039
  helix:  1.42 (0.24), residues: 467
  sheet: -0.52 (0.36), residues: 199
  loop : -0.41 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 810 
 TYR   0.023   0.001   TYR G  52 
 PHE   0.017   0.002   PHE C  13 
 TRP   0.008   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12530)
  covalent geometry    : angle       0.57298 (17704)
  hydrogen bonds       : bond        0.03475 (  593)
  hydrogen bonds       : angle       4.14987 ( 1561)

*********************** 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  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8044 (m-30) cc_final: 0.7670 (t70)
REVERT: G   31 ASN cc_start: 0.8224 (m-40) cc_final: 0.7886 (m-40)
REVERT: H    1 MET cc_start: 0.7203 (tpt) cc_final: 0.6868 (tpt)
REVERT: H  190 TYR cc_start: 0.8237 (m-80) cc_final: 0.7818 (m-80)
REVERT: H  278 MET cc_start: 0.7996 (mmp) cc_final: 0.7751 (mmm)
REVERT: H  596 GLU cc_start: 0.5843 (tm-30) cc_final: 0.5297 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 128
  average time/residue: 0.0877
  time to fit residues: 17.3080
Evaluate side-chains
  120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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   56 ASN
Chi-restraints excluded: chain E residue   62 TYR
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   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  649 MET
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 62 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.079097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.060667 restraints weight = 49141.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.060920 restraints weight = 38431.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.061417 restraints weight = 23468.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.061652 restraints weight = 21741.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.061794 restraints weight = 17965.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12530  Z= 0.229
  Angle     :  0.621   5.380  17704  Z= 0.357
  Chirality :  0.038   0.142   1988
  Planarity :  0.004   0.040   1651
  Dihedral  : 27.563 176.055   3232
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.23 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.26), residues: 1039
  helix:  1.41 (0.24), residues: 459
  sheet: -0.68 (0.36), residues: 201
  loop : -0.60 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  63 
 TYR   0.028   0.002   TYR G  52 
 PHE   0.023   0.002   PHE C  13 
 TRP   0.007   0.001   TRP H 277 
 HIS   0.004   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (12530)
  covalent geometry    : angle       0.62094 (17704)
  hydrogen bonds       : bond        0.04026 (  593)
  hydrogen bonds       : angle       4.32653 ( 1561)

*********************** 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
  136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 102
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 ASP cc_start: 0.8263 (m-30) cc_final: 0.7607 (t70)
REVERT: E   95 ASP cc_start: 0.8027 (m-30) cc_final: 0.7366 (m-30)
REVERT: G   31 ASN cc_start: 0.8188 (m-40) cc_final: 0.7824 (m110)
REVERT: H    1 MET cc_start: 0.7154 (tpt) cc_final: 0.6915 (tpt)
REVERT: H    2 MET cc_start: 0.7495 (ttp) cc_final: 0.7026 (tmm)
REVERT: H  190 TYR cc_start: 0.7967 (m-80) cc_final: 0.7715 (m-80)
REVERT: H  596 GLU cc_start: 0.6031 (tm-30) cc_final: 0.5644 (tm-30)
  outliers start: 34
  outliers final: 28
  residues processed: 125
  average time/residue: 0.0980
  time to fit residues: 19.1818
Evaluate side-chains
  126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   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   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  276 GLU
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0980
   chunk 118 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.080362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.060520 restraints weight = 49316.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.062070 restraints weight = 26799.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.063040 restraints weight = 18250.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.063650 restraints weight = 14407.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.063984 restraints weight = 12449.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12530  Z= 0.154
  Angle     :  0.565   5.713  17704  Z= 0.328
  Chirality :  0.035   0.158   1988
  Planarity :  0.004   0.040   1651
  Dihedral  : 27.339 175.830   3232
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 12.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1039
  helix:  1.54 (0.24), residues: 467
  sheet: -0.53 (0.37), residues: 199
  loop : -0.42 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.027   0.001   TYR G  52 
 PHE   0.025   0.001   PHE F  39 
 TRP   0.008   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12530)
  covalent geometry    : angle       0.56489 (17704)
  hydrogen bonds       : bond        0.03456 (  593)
  hydrogen bonds       : angle       4.07147 ( 1561)

*********************** 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
  145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   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: 0.7690 (t70)
REVERT: E   95 ASP cc_start: 0.7823 (m-30) cc_final: 0.7294 (m-30)
REVERT: G   31 ASN cc_start: 0.8297 (m-40) cc_final: 0.7896 (m-40)
REVERT: H    1 MET cc_start: 0.7336 (tpt) cc_final: 0.7062 (tpt)
REVERT: H  190 TYR cc_start: 0.8084 (m-80) cc_final: 0.7799 (m-80)
REVERT: H  278 MET cc_start: 0.8149 (mmm) cc_final: 0.7920 (mmt)
  outliers start: 33
  outliers final: 27
  residues processed: 134
  average time/residue: 0.0968
  time to fit residues: 20.2590
Evaluate side-chains
  127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 GLU
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   18 LEU
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 F residue   46 LYS
Chi-restraints excluded: chain F residue   56 ASN
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 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 91 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:
D  54 HIS
H 145 ASN
H 193 GLN
** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.080044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.061558 restraints weight = 49266.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.062215 restraints weight = 34368.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.062307 restraints weight = 21924.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.062671 restraints weight = 20956.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.062826 restraints weight = 17740.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12530  Z= 0.220
  Angle     :  0.611   6.475  17704  Z= 0.351
  Chirality :  0.037   0.142   1988
  Planarity :  0.004   0.037   1651
  Dihedral  : 27.487 176.650   3232
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.26), residues: 1039
  helix:  1.55 (0.24), residues: 459
  sheet: -0.75 (0.36), residues: 203
  loop : -0.60 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  63 
 TYR   0.035   0.002   TYR G  52 
 PHE   0.029   0.002   PHE F  39 
 TRP   0.006   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (12530)
  covalent geometry    : angle       0.61140 (17704)
  hydrogen bonds       : bond        0.03872 (  593)
  hydrogen bonds       : angle       4.24164 ( 1561)

*********************** 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: 34
    poor density    : 101
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7760 (t0) cc_final: 0.7519 (t0)
REVERT: D   68 ASP cc_start: 0.8172 (m-30) cc_final: 0.7713 (t70)
REVERT: E   95 ASP cc_start: 0.8011 (m-30) cc_final: 0.7383 (m-30)
REVERT: G   31 ASN cc_start: 0.8217 (m-40) cc_final: 0.7857 (m-40)
REVERT: H    1 MET cc_start: 0.7378 (tpt) cc_final: 0.7134 (tpt)
REVERT: H    2 MET cc_start: 0.7861 (ttp) cc_final: 0.7224 (tmm)
REVERT: H  190 TYR cc_start: 0.7883 (m-80) cc_final: 0.7676 (m-80)
REVERT: H  278 MET cc_start: 0.8183 (mmm) cc_final: 0.7929 (mmt)
  outliers start: 34
  outliers final: 30
  residues processed: 125
  average time/residue: 0.0946
  time to fit residues: 18.5703
Evaluate side-chains
  129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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   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   46 LYS
Chi-restraints excluded: chain F residue   56 ASN
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  183 THR
Chi-restraints excluded: chain H residue  229 VAL
Chi-restraints excluded: chain H residue  276 GLU
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 36 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN
** 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 = 0.080339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061822 restraints weight = 49386.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062400 restraints weight = 34634.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062454 restraints weight = 22587.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.062840 restraints weight = 21512.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.063058 restraints weight = 18065.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.4536

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= 0.200
  Angle     :  0.599   6.730  17704  Z= 0.345
  Chirality :  0.037   0.159   1988
  Planarity :  0.004   0.036   1651
  Dihedral  : 27.462 176.725   3232
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 14.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.26), residues: 1039
  helix:  1.51 (0.24), residues: 460
  sheet: -0.66 (0.35), residues: 219
  loop : -0.62 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  63 
 TYR   0.035   0.002   TYR G  52 
 PHE   0.031   0.002   PHE F  39 
 TRP   0.008   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (12530)
  covalent geometry    : angle       0.59924 (17704)
  hydrogen bonds       : bond        0.03746 (  593)
  hydrogen bonds       : angle       4.22054 ( 1561)

*********************** 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: 32
    poor density    : 100
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7746 (t0) cc_final: 0.7516 (t0)
REVERT: D   68 ASP cc_start: 0.8217 (m-30) cc_final: 0.7730 (t70)
REVERT: E   95 ASP cc_start: 0.7949 (m-30) cc_final: 0.7325 (m-30)
REVERT: G   31 ASN cc_start: 0.8189 (m-40) cc_final: 0.7814 (m-40)
REVERT: H    1 MET cc_start: 0.7454 (tpt) cc_final: 0.7201 (tpt)
REVERT: H    2 MET cc_start: 0.7929 (ttp) cc_final: 0.7221 (tmm)
REVERT: H  274 MET cc_start: 0.7795 (mmm) cc_final: 0.7551 (tpt)
REVERT: H  278 MET cc_start: 0.8152 (mmm) cc_final: 0.7888 (mmt)
  outliers start: 32
  outliers final: 30
  residues processed: 123
  average time/residue: 0.0971
  time to fit residues: 18.7546
Evaluate side-chains
  130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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   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   22 VAL
Chi-restraints excluded: chain F residue   46 LYS
Chi-restraints excluded: chain F residue   56 ASN
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 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  229 VAL
Chi-restraints excluded: chain H residue  276 GLU
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 100 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.081056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.062733 restraints weight = 49010.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063126 restraints weight = 32251.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.063575 restraints weight = 21668.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.064084 restraints weight = 20197.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.064038 restraints weight = 17426.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.4629

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= 0.164
  Angle     :  0.582   7.364  17704  Z= 0.336
  Chirality :  0.036   0.145   1988
  Planarity :  0.004   0.035   1651
  Dihedral  : 27.414 177.146   3232
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1039
  helix:  1.58 (0.24), residues: 460
  sheet: -0.61 (0.36), residues: 213
  loop : -0.63 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.031   0.002   TYR G  52 
 PHE   0.037   0.002   PHE F  39 
 TRP   0.009   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12530)
  covalent geometry    : angle       0.58151 (17704)
  hydrogen bonds       : bond        0.03541 (  593)
  hydrogen bonds       : angle       4.12719 ( 1561)

*********************** 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
  133 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7729 (t0) cc_final: 0.7514 (t0)
REVERT: D   68 ASP cc_start: 0.8177 (m-30) cc_final: 0.7726 (t70)
REVERT: E   95 ASP cc_start: 0.7890 (m-30) cc_final: 0.7264 (m-30)
REVERT: G   31 ASN cc_start: 0.8270 (m-40) cc_final: 0.7924 (m-40)
REVERT: H    1 MET cc_start: 0.7493 (tpt) cc_final: 0.7281 (tpt)
REVERT: H    2 MET cc_start: 0.7880 (ttp) cc_final: 0.7219 (tmm)
REVERT: H  274 MET cc_start: 0.7832 (mmm) cc_final: 0.7613 (tpt)
REVERT: H  278 MET cc_start: 0.8205 (mmm) cc_final: 0.7941 (mmt)
  outliers start: 30
  outliers final: 28
  residues processed: 124
  average time/residue: 0.0949
  time to fit residues: 18.4980
Evaluate side-chains
  127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   18 LEU
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 F residue   18 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 LYS
Chi-restraints excluded: chain F residue   56 ASN
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 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  276 GLU
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 52 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.080827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.062437 restraints weight = 48982.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.062826 restraints weight = 32846.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.063243 restraints weight = 21784.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.063856 restraints weight = 20503.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.063811 restraints weight = 17528.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4715

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= 0.176
  Angle     :  0.587   6.685  17704  Z= 0.339
  Chirality :  0.036   0.142   1988
  Planarity :  0.004   0.035   1651
  Dihedral  : 27.423 176.881   3232
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.73 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.26), residues: 1039
  helix:  1.59 (0.24), residues: 460
  sheet: -0.66 (0.35), residues: 215
  loop : -0.62 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.033   0.001   TYR G  52 
 PHE   0.016   0.001   PHE C  13 
 TRP   0.008   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (12530)
  covalent geometry    : angle       0.58715 (17704)
  hydrogen bonds       : bond        0.03647 (  593)
  hydrogen bonds       : angle       4.14065 ( 1561)

********************** 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
  128 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7726 (t0) cc_final: 0.7484 (t0)
REVERT: D   68 ASP cc_start: 0.8212 (m-30) cc_final: 0.7755 (t70)
REVERT: E   95 ASP cc_start: 0.7925 (m-30) cc_final: 0.7285 (m-30)
REVERT: G   31 ASN cc_start: 0.8287 (m-40) cc_final: 0.7928 (m-40)
REVERT: H    1 MET cc_start: 0.7448 (tpt) cc_final: 0.7218 (tpt)
REVERT: H    2 MET cc_start: 0.7895 (ttp) cc_final: 0.7202 (tmm)
REVERT: H  274 MET cc_start: 0.7877 (mmm) cc_final: 0.7671 (tpt)
REVERT: H  278 MET cc_start: 0.8211 (mmm) cc_final: 0.7970 (mmt)
  outliers start: 29
  outliers final: 26
  residues processed: 119
  average time/residue: 0.0915
  time to fit residues: 17.5551
Evaluate side-chains
  124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   46 LYS
Chi-restraints excluded: chain F residue   56 ASN
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 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  276 GLU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 44 optimal weight:    0.0570
   chunk 0 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 113 optimal weight:    0.3980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.081557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.063347 restraints weight = 49267.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063604 restraints weight = 33165.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.064044 restraints weight = 21922.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.064481 restraints weight = 20999.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.064461 restraints weight = 18116.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4818

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= 0.152
  Angle     :  0.573   7.775  17704  Z= 0.331
  Chirality :  0.035   0.165   1988
  Planarity :  0.003   0.035   1651
  Dihedral  : 27.350 179.126   3232
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.08 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1039
  helix:  1.68 (0.24), residues: 459
  sheet: -0.74 (0.38), residues: 195
  loop : -0.61 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  63 
 TYR   0.034   0.002   TYR G  52 
 PHE   0.039   0.001   PHE F  39 
 TRP   0.014   0.001   TRP H 638 
 HIS   0.003   0.001   HIS H 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12530)
  covalent geometry    : angle       0.57308 (17704)
  hydrogen bonds       : bond        0.03492 (  593)
  hydrogen bonds       : angle       4.03410 ( 1561)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2420.44 seconds
wall clock time: 42 minutes 35.66 seconds (2555.66 seconds total)