Starting phenix.real_space_refine
on Thu May 15 03:10:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y60_33630/05_2025/7y60_33630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y60_33630/05_2025/7y60_33630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y60_33630/05_2025/7y60_33630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y60_33630/05_2025/7y60_33630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y60_33630/05_2025/7y60_33630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y60_33630/05_2025/7y60_33630.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1848 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     216      5.49       5
     S      20      5.16       5
     C    6418      2.51       5
     N    2172      2.21       5
     O    2552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11378
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "G"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "H"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 595
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 761
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 591
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "I"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2198
          Classifications: {'DNA': 108}
          Link IDs: {'rna3p': 107}
    Chain: "C"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 732
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "D"
      Number of atoms: 583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 583
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 602
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
    Chain: "J"
      Number of atoms: 2230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2230
          Classifications: {'DNA': 108}
          Link IDs: {'rna3p': 107}
    Chain: "K"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 99
          Classifications: {'peptide': 20}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 18}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "L"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 1749
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 309}
          Link IDs: {'PTRANS': 13, 'TRANS': 340}
          Chain breaks: 4
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 1113
          Unresolved non-hydrogen angles: 1439
          Unresolved non-hydrogen dihedrals: 949
          Unresolved non-hydrogen chiralities: 104
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 18, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 8, 'ASP:plan': 22, 'PHE:plan': 17, 'GLU:plan': 14, 'HIS:plan': 10}
          Unresolved non-hydrogen planarities: 600
  Time building chain proxies: 6.98, per 1000 atoms: 0.61
  Number of scatterers: 11378
  At special positions: 0
  Unit cell: (107, 116, 122, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     216     15.00
     O    2552      8.00
     N    2172      7.00
     C    6418      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1896

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      49.4% alpha, 15.4% beta
      97 base pairs and 169 stacking pairs defined.
    Time for finding SS restraints: 4.62
  Creating SS restraints...
    Processing helix  chain 'G' and resid 63 through 79
    Processing helix  chain 'G' and resid 85 through 114
      removed outlier: 3.786A  pdb=" N   ALA G 114 " --> pdb=" O   CYS G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.573A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 29
    Processing helix  chain 'H' and resid 30 through 42
    Processing helix  chain 'H' and resid 49 through 77
      removed outlier: 4.122A  pdb=" N   ARG H  55 " --> pdb=" O   TYR H  51 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN H  64 " --> pdb=" O   VAL H  60 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL H  65 " --> pdb=" O   PHE H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 94
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.820A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.325A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.735A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 57
      removed outlier: 3.787A  pdb=" N   SER C  57 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 77
      removed outlier: 3.736A  pdb=" N   ASP C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 131
      removed outlier: 3.502A  pdb=" N   ILE C 124 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG C 131 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.761A  pdb=" N   ARG D  55 " --> pdb=" O   TYR D  51 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   GLY D  56 " --> pdb=" O   GLU D  52 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL D  57 " --> pdb=" O   GLU D  53 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASN D  64 " --> pdb=" O   VAL D  60 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ARG D  67 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   THR D  71 " --> pdb=" O   ARG D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.736A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.505A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 4.054A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 4.703A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 4.201A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 703 through 707
      removed outlier: 3.643A  pdb=" N   GLN K 706 " --> pdb=" O   VAL K 703 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.831A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84
      removed outlier: 6.917A  pdb=" N   ARG C  83 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 5
      removed outlier: 6.881A  pdb=" N   PHE L 360 " --> pdb=" O   TRP L 354 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   TRP L 354 " --> pdb=" O   PHE L 360 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA L 362 " --> pdb=" O   ILE L 352 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ILE L 352 " --> pdb=" O   ALA L 362 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER L 364 " --> pdb=" O   SER L 350 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 21
      removed outlier: 6.606A  pdb=" N   ALA L  35 " --> pdb=" O   TYR L  17 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LEU L  19 " --> pdb=" O   ALA L  33 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ALA L  33 " --> pdb=" O   LEU L  19 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   PHE L  21 " --> pdb=" O   ARG L  31 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ARG L  31 " --> pdb=" O   PHE L  21 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL L  41 " --> pdb=" O   ASN L  61 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   ASN L  61 " --> pdb=" O   VAL L  41 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE L  43 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74
      removed outlier: 6.226A  pdb=" N   ILE L  90 " --> pdb=" O   THR L 124 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   THR L 124 " --> pdb=" O   ILE L  90 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU L  92 " --> pdb=" O   VAL L 122 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137
      removed outlier: 6.220A  pdb=" N   ASP L 157 " --> pdb=" O   LYS L 163 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   LYS L 163 " --> pdb=" O   ASP L 157 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179
      removed outlier: 3.617A  pdb=" N   GLY L 176 " --> pdb=" O   LEU L 189 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU L 195 " --> pdb=" O   ASN L 208 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASN L 208 " --> pdb=" O   LEU L 195 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL L 197 " --> pdb=" O   ALA L 206 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG L 204 " --> pdb=" O   SER L 199 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 211 through 213
    Processing sheet with id=AB1, first strand: chain 'L' and resid 241 through 242
      removed outlier: 3.822A  pdb=" N   ALA L 253 " --> pdb=" O   THR L 265 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   THR L 265 " --> pdb=" O   ALA L 253 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   CYS L 255 " --> pdb=" O   MET L 263 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   MET L 263 " --> pdb=" O   CYS L 255 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA L 279 " --> pdb=" O   VAL L 268 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 288 through 299
      removed outlier: 5.542A  pdb=" N   VAL L 318 " --> pdb=" O   CYS L 294 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   VAL L 296 " --> pdb=" O   ARG L 316 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ARG L 316 " --> pdb=" O   VAL L 296 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   SER L 326 " --> pdb=" O   SER L 323 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      239 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      97 basepair parallelities
      169 stacking parallelities
  Total time for adding SS restraints: 4.90

  Time building geometry restraints manager: 3.33 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: 2326
        1.33 -     1.45: 3591
        1.45 -     1.58: 5584
        1.58 -     1.70: 430
        1.70 -     1.82: 32
  Bond restraints: 11963
  Sorted by residual:
  bond pdb=" C   ARG G  63 "
       pdb=" O   ARG G  63 "
    ideal  model  delta    sigma   weight residual
    1.234  1.210  0.025 1.20e-02 6.94e+03 4.27e+00
  bond pdb=" N   ARG G  63 "
       pdb=" CA  ARG G  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.479 -0.022 1.28e-02 6.10e+03 3.09e+00
  bond pdb=" CD  ARG G  63 "
       pdb=" NE  ARG G  63 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.40e-02 5.10e+03 2.87e+00
  bond pdb=" C   LEU G  65 "
       pdb=" O   LEU G  65 "
    ideal  model  delta    sigma   weight residual
    1.244  1.229  0.014 9.80e-03 1.04e+04 2.17e+00
  bond pdb=" C3'  DC I  79 "
       pdb=" O3'  DC I  79 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.05e+00
  ... (remaining 11958 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 16916
        2.30 -     4.59: 173
        4.59 -     6.89: 26
        6.89 -     9.18: 7
        9.18 -    11.48: 1
  Bond angle restraints: 17123
  Sorted by residual:
  angle pdb=" C   LEU G  65 "
        pdb=" N   PRO G  66 "
        pdb=" CA  PRO G  66 "
      ideal   model   delta    sigma   weight residual
     118.85  127.59   -8.74 1.09e+00 8.42e-01 6.44e+01
  angle pdb=" N   LYS G  64 "
        pdb=" CA  LYS G  64 "
        pdb=" C   LYS G  64 "
      ideal   model   delta    sigma   weight residual
     111.28  119.29   -8.01 1.09e+00 8.42e-01 5.40e+01
  angle pdb=" O3'  DC I  84 "
        pdb=" C3'  DC I  84 "
        pdb=" C2'  DC I  84 "
      ideal   model   delta    sigma   weight residual
     111.50  102.59    8.91 1.50e+00 4.44e-01 3.53e+01
  angle pdb=" CA  LEU G  65 "
        pdb=" C   LEU G  65 "
        pdb=" N   PRO G  66 "
      ideal   model   delta    sigma   weight residual
     120.93  116.13    4.80 1.06e+00 8.90e-01 2.05e+01
  angle pdb=" C   ARG G  63 "
        pdb=" CA  ARG G  63 "
        pdb=" CB  ARG G  63 "
      ideal   model   delta    sigma   weight residual
     109.90  116.83   -6.93 1.56e+00 4.11e-01 1.97e+01
  ... (remaining 17118 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.09: 5462
       35.09 -    70.17: 1123
       70.17 -   105.26: 37
      105.26 -   140.34: 0
      140.34 -   175.43: 4
  Dihedral angle restraints: 6626
    sinusoidal: 3721
      harmonic: 2905
  Sorted by residual:
  dihedral pdb=" CA  PHE K 711 "
           pdb=" C   PHE K 711 "
           pdb=" N   LEU K 712 "
           pdb=" CA  LEU K 712 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.46   22.54     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" C4'  DC I  82 "
           pdb=" C3'  DC I  82 "
           pdb=" O3'  DC I  82 "
           pdb=" P    DG I  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.57  175.43     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC I  79 "
           pdb=" C3'  DC I  79 "
           pdb=" O3'  DC I  79 "
           pdb=" P    DC I  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.97 -173.97     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 6623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1657
       0.049 -    0.097: 294
       0.097 -    0.146: 66
       0.146 -    0.194: 3
       0.194 -    0.243: 1
  Chirality restraints: 2021
  Sorted by residual:
  chirality pdb=" CA  LYS G  64 "
            pdb=" N   LYS G  64 "
            pdb=" C   LYS G  64 "
            pdb=" CB  LYS G  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CG  LEU F  37 "
            pdb=" CB  LEU F  37 "
            pdb=" CD1 LEU F  37 "
            pdb=" CD2 LEU F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" C3'  DC I  84 "
            pdb=" C4'  DC I  84 "
            pdb=" O3'  DC I  84 "
            pdb=" C2'  DC I  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.38e-01
  ... (remaining 2018 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G  63 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   ARG G  63 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG G  63 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS G  64 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G  82 "   -0.008 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   LEU G  82 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU G  82 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG G  83 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU G  65 "   -0.028 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO G  66 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO G  66 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO G  66 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1111
        2.74 -     3.28: 10944
        3.28 -     3.82: 21860
        3.82 -     4.36: 23489
        4.36 -     4.90: 34819
  Nonbonded interactions: 92223
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  56 "
            pdb=" N2   DG J  92 "
     model   vdw
     2.200 2.496
  nonbonded pdb=" N2   DG I  37 "
            pdb=" O2   DC J 111 "
     model   vdw
     2.219 2.496
  nonbonded pdb=" O2   DC I  54 "
            pdb=" N2   DG J  94 "
     model   vdw
     2.231 2.496
  nonbonded pdb=" N2   DG I  67 "
            pdb=" O2   DC J  81 "
     model   vdw
     2.239 2.496
  nonbonded pdb=" OG1 THR E 118 "
            pdb=" NH1 ARG F  45 "
     model   vdw
     2.240 3.120
  ... (remaining 92218 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 59 through 134)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'B' and resid 26 through 97)
  selection = (chain 'D' and resid 26 through 97)
  selection = (chain 'F' and resid 26 through 97)
  selection = (chain 'H' and resid 26 through 97)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.160
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
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      :  0.004   0.043  11963  Z= 0.170
  Angle     :  0.674  11.477  17123  Z= 0.397
  Chirality :  0.040   0.243   2021
  Planarity :  0.004   0.048   1458
  Dihedral  : 28.445 175.426   4730
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 34.39 %
    Favored  : 64.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 974
  helix:  0.66 (0.24), residues: 461
  sheet:  0.40 (0.45), residues: 132
  loop : -1.04 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.009   0.003   HIS C 113 
 PHE   0.022   0.001   PHE G  84 
 TYR   0.019   0.001   TYR C  99 
 ARG   0.014   0.001   ARG F  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14707 (  669)
  hydrogen bonds       : angle       5.61335 ( 1689)
  covalent geometry    : bond        0.00360 (11963)
  covalent geometry    : angle       0.67430 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 236
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  109 LEU cc_start: 0.8749 (mt) cc_final: 0.8334 (mp)
REVERT: F   88 TYR cc_start: 0.7381 (m-80) cc_final: 0.6741 (m-80)
REVERT: D   68 ASP cc_start: 0.6511 (p0) cc_final: 0.5584 (p0)
REVERT: D   77 LYS cc_start: 0.7997 (tptp) cc_final: 0.7789 (tppt)
REVERT: A   90 MET cc_start: 0.8241 (mtm) cc_final: 0.7022 (mtm)
  outliers start: 7
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2857
  time to fit residues: 89.6944
Evaluate side-chains
  152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:   40.0000
   chunk 87 optimal weight:   50.0000
   chunk 48 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 105 optimal weight:   50.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
** A  68 GLN ** 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 = 0.3445 r_free = 0.3445 target = 0.050002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.033410 restraints weight = 87233.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.034466 restraints weight = 48783.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.035152 restraints weight = 34316.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
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      :  0.008   0.056  11963  Z= 0.374
  Angle     :  0.773   8.557  17123  Z= 0.441
  Chirality :  0.045   0.201   2021
  Planarity :  0.005   0.049   1458
  Dihedral  : 31.243 177.432   3422
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 25.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  8.55 %
    Allowed  : 29.74 %
    Favored  : 61.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 974
  helix:  0.74 (0.23), residues: 476
  sheet:  0.58 (0.45), residues: 131
  loop : -0.90 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.009   0.003   HIS G 113 
 PHE   0.027   0.002   PHE E  67 
 TYR   0.018   0.002   TYR C  99 
 ARG   0.008   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09569 (  669)
  hydrogen bonds       : angle       4.43274 ( 1689)
  covalent geometry    : bond        0.00810 (11963)
  covalent geometry    : angle       0.77304 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 173
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   60 LEU cc_start: 0.8892 (pt) cc_final: 0.8632 (pt)
REVERT: G   62 ILE cc_start: 0.9667 (mp) cc_final: 0.9399 (pt)
REVERT: G   70 LEU cc_start: 0.9726 (tp) cc_final: 0.9183 (mt)
REVERT: G   73 GLU cc_start: 0.8068 (tt0) cc_final: 0.7790 (mt-10)
REVERT: G   90 MET cc_start: 0.8665 (tmm) cc_final: 0.8437 (tmm)
REVERT: H   26 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9476 (mm)
REVERT: H   63 GLU cc_start: 0.9084 (pp20) cc_final: 0.8779 (pp20)
REVERT: E   64 LYS cc_start: 0.9631 (mmmm) cc_final: 0.9427 (mmmm)
REVERT: F   31 LYS cc_start: 0.9671 (OUTLIER) cc_final: 0.9431 (ttmm)
REVERT: F   63 GLU cc_start: 0.9117 (tp30) cc_final: 0.8456 (tp30)
REVERT: F   67 ARG cc_start: 0.8598 (ttm110) cc_final: 0.8082 (ttm110)
REVERT: F   84 MET cc_start: 0.9363 (tpp) cc_final: 0.8864 (tpp)
REVERT: F   88 TYR cc_start: 0.9440 (m-80) cc_final: 0.8811 (m-80)
REVERT: C   54 TYR cc_start: 0.9164 (m-80) cc_final: 0.8882 (m-80)
REVERT: C   80 THR cc_start: 0.9139 (m) cc_final: 0.8694 (m)
REVERT: C   94 GLU cc_start: 0.9384 (tp30) cc_final: 0.8316 (tp30)
REVERT: C  105 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9297 (mm-30)
REVERT: D   25 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8856 (p0)
REVERT: D   77 LYS cc_start: 0.9697 (tptp) cc_final: 0.9469 (tppt)
REVERT: D   84 MET cc_start: 0.9008 (tpp) cc_final: 0.8506 (tmm)
REVERT: A   90 MET cc_start: 0.8858 (mtm) cc_final: 0.8397 (mtm)
REVERT: A   94 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8743 (mm-30)
REVERT: A  120 MET cc_start: 0.8500 (mmt) cc_final: 0.8216 (mmt)
REVERT: A  128 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.8996 (mmm-85)
REVERT: A  133 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: B   53 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8754 (mm-30)
  outliers start: 46
  outliers final: 26
  residues processed: 209
  average time/residue: 0.2686
  time to fit residues: 76.4816
Evaluate side-chains
  175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   78 PHE
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  118 THR
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 110 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 98 optimal weight:   40.0000
   chunk 115 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 91 optimal weight:   50.0000
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.049898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.033650 restraints weight = 87784.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.034732 restraints weight = 47898.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.035431 restraints weight = 33176.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  11963  Z= 0.273
  Angle     :  0.709  11.368  17123  Z= 0.403
  Chirality :  0.042   0.166   2021
  Planarity :  0.004   0.039   1458
  Dihedral  : 31.405 176.961   3422
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 21.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 33.27 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 974
  helix:  0.90 (0.23), residues: 475
  sheet:  0.53 (0.43), residues: 139
  loop : -0.81 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.002   HIS C 113 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.013   0.001   TYR H  88 
 ARG   0.006   0.001   ARG E  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07280 (  669)
  hydrogen bonds       : angle       4.11403 ( 1689)
  covalent geometry    : bond        0.00592 (11963)
  covalent geometry    : angle       0.70874 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 GLU cc_start: 0.8318 (tt0) cc_final: 0.7484 (mt-10)
REVERT: E   64 LYS cc_start: 0.9631 (mmmm) cc_final: 0.9416 (mmmm)
REVERT: E   68 GLN cc_start: 0.9732 (tt0) cc_final: 0.9379 (tp-100)
REVERT: E  120 MET cc_start: 0.9355 (mmm) cc_final: 0.9039 (mmm)
REVERT: F   63 GLU cc_start: 0.9115 (tp30) cc_final: 0.8729 (tp30)
REVERT: F   84 MET cc_start: 0.9322 (tpp) cc_final: 0.8759 (tpp)
REVERT: F   88 TYR cc_start: 0.9430 (m-80) cc_final: 0.8846 (m-80)
REVERT: C   54 TYR cc_start: 0.9011 (m-80) cc_final: 0.8804 (m-80)
REVERT: C   94 GLU cc_start: 0.8906 (tp30) cc_final: 0.8513 (tp30)
REVERT: C  105 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9166 (mm-30)
REVERT: C  110 CYS cc_start: 0.9757 (m) cc_final: 0.9433 (m)
REVERT: D   25 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8566 (p0)
REVERT: D   63 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9122 (mm-30)
REVERT: D   77 LYS cc_start: 0.9690 (tptp) cc_final: 0.9473 (tppt)
REVERT: D   84 MET cc_start: 0.8978 (tpp) cc_final: 0.8345 (tmm)
REVERT: D   91 LYS cc_start: 0.9376 (tttp) cc_final: 0.9031 (tptt)
REVERT: A   90 MET cc_start: 0.8888 (mtm) cc_final: 0.8393 (mtm)
REVERT: A   94 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8803 (mm-30)
REVERT: A   97 GLU cc_start: 0.9300 (tm-30) cc_final: 0.9027 (pp20)
REVERT: A  120 MET cc_start: 0.8725 (mmt) cc_final: 0.8303 (mmm)
REVERT: A  128 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.8824 (mmm-85)
REVERT: B   53 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8630 (mm-30)
REVERT: B   64 ASN cc_start: 0.9749 (m110) cc_final: 0.9458 (p0)
  outliers start: 32
  outliers final: 20
  residues processed: 187
  average time/residue: 0.2580
  time to fit residues: 66.0895
Evaluate side-chains
  165 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 100 optimal weight:   50.0000
   chunk 58 optimal weight:    5.9990
   chunk 113 optimal weight:   40.0000
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 81 optimal weight:   50.0000
   chunk 63 optimal weight:    0.1980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
C  55 GLN
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
D  25 ASN
A  76 GLN
B  64 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.064669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.049284 restraints weight = 110318.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.050575 restraints weight = 53442.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.051380 restraints weight = 34647.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11963  Z= 0.159
  Angle     :  0.663  11.231  17123  Z= 0.376
  Chirality :  0.041   0.263   2021
  Planarity :  0.003   0.033   1458
  Dihedral  : 31.053 175.392   3422
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 33.83 %
    Favored  : 60.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.27), residues: 974
  helix:  1.06 (0.24), residues: 478
  sheet:  0.59 (0.43), residues: 145
  loop : -0.68 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.002   HIS C 113 
 PHE   0.010   0.001   PHE C 104 
 TYR   0.009   0.001   TYR H  88 
 ARG   0.007   0.001   ARG G  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06362 (  669)
  hydrogen bonds       : angle       3.68448 ( 1689)
  covalent geometry    : bond        0.00344 (11963)
  covalent geometry    : angle       0.66279 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9673 (tp) cc_final: 0.9131 (mt)
REVERT: G   73 GLU cc_start: 0.7785 (tt0) cc_final: 0.7309 (mt-10)
REVERT: G  120 MET cc_start: 0.9017 (mmt) cc_final: 0.8802 (mmm)
REVERT: H   63 GLU cc_start: 0.9281 (pp20) cc_final: 0.8710 (pp20)
REVERT: E   64 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9400 (mmmm)
REVERT: E   68 GLN cc_start: 0.9672 (tt0) cc_final: 0.9313 (tp40)
REVERT: E  105 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9075 (mm-30)
REVERT: F   74 GLU cc_start: 0.8664 (pp20) cc_final: 0.8441 (pp20)
REVERT: F   84 MET cc_start: 0.9167 (tpp) cc_final: 0.8499 (tpp)
REVERT: F   88 TYR cc_start: 0.9368 (m-80) cc_final: 0.8710 (m-80)
REVERT: C   54 TYR cc_start: 0.9011 (m-80) cc_final: 0.8801 (m-80)
REVERT: C   94 GLU cc_start: 0.8817 (tp30) cc_final: 0.8281 (tp30)
REVERT: C   97 GLU cc_start: 0.8034 (pp20) cc_final: 0.7769 (pp20)
REVERT: C  110 CYS cc_start: 0.9703 (m) cc_final: 0.9446 (m)
REVERT: D   25 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8260 (p0)
REVERT: D   63 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9036 (mm-30)
REVERT: D   77 LYS cc_start: 0.9686 (tptp) cc_final: 0.9476 (tppt)
REVERT: D   84 MET cc_start: 0.8835 (tpp) cc_final: 0.8420 (tmm)
REVERT: D   85 ASP cc_start: 0.8839 (m-30) cc_final: 0.8533 (t0)
REVERT: A   90 MET cc_start: 0.9035 (mtm) cc_final: 0.8699 (mtt)
REVERT: A   94 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: A   97 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8958 (pp20)
REVERT: A  120 MET cc_start: 0.8620 (mmt) cc_final: 0.8132 (mmm)
REVERT: A  128 ARG cc_start: 0.9230 (mmm-85) cc_final: 0.8350 (mmm-85)
REVERT: A  133 GLU cc_start: 0.8660 (mp0) cc_final: 0.8301 (mp0)
REVERT: B   52 GLU cc_start: 0.9302 (pm20) cc_final: 0.9030 (pm20)
REVERT: B   53 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8800 (mm-30)
REVERT: B   55 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8571 (mmm-85)
  outliers start: 30
  outliers final: 17
  residues processed: 194
  average time/residue: 0.2572
  time to fit residues: 68.0668
Evaluate side-chains
  173 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 86 optimal weight:   30.0000
   chunk 105 optimal weight:   50.0000
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 88 optimal weight:   50.0000
   chunk 87 optimal weight:   40.0000
   chunk 68 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    5.5586

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
** A  76 GLN ** 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 = 0.3412 r_free = 0.3412 target = 0.047955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.031680 restraints weight = 90546.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.032715 restraints weight = 50200.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.033358 restraints weight = 35132.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  11963  Z= 0.328
  Angle     :  0.736  10.680  17123  Z= 0.420
  Chirality :  0.044   0.257   2021
  Planarity :  0.004   0.031   1458
  Dihedral  : 31.573 179.174   3422
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 24.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 33.83 %
    Favored  : 58.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.27), residues: 974
  helix:  0.93 (0.23), residues: 475
  sheet:  0.86 (0.46), residues: 130
  loop : -0.62 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.012   0.002   PHE E  67 
 TYR   0.013   0.002   TYR C  99 
 ARG   0.008   0.001   ARG G  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08331 (  669)
  hydrogen bonds       : angle       4.20670 ( 1689)
  covalent geometry    : bond        0.00714 (11963)
  covalent geometry    : angle       0.73649 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9681 (tp) cc_final: 0.9101 (mt)
REVERT: G   73 GLU cc_start: 0.7982 (tt0) cc_final: 0.7343 (mt-10)
REVERT: H   39 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8607 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9641 (mmmm) cc_final: 0.9425 (mmmm)
REVERT: F   63 GLU cc_start: 0.8857 (tp30) cc_final: 0.8536 (tp30)
REVERT: F   74 GLU cc_start: 0.8808 (pp20) cc_final: 0.8581 (pp20)
REVERT: F   84 MET cc_start: 0.9317 (tpp) cc_final: 0.8760 (tpp)
REVERT: F   88 TYR cc_start: 0.9471 (m-80) cc_final: 0.8994 (m-80)
REVERT: C   54 TYR cc_start: 0.9072 (m-80) cc_final: 0.8538 (m-80)
REVERT: C   83 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7181 (tpt90)
REVERT: C   94 GLU cc_start: 0.9044 (tp30) cc_final: 0.8527 (tp30)
REVERT: C   97 GLU cc_start: 0.8301 (pp20) cc_final: 0.8061 (pp20)
REVERT: C  105 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9183 (mm-30)
REVERT: D   25 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8840 (p0)
REVERT: D   63 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9152 (mm-30)
REVERT: D   84 MET cc_start: 0.8959 (tpp) cc_final: 0.8315 (tmm)
REVERT: D   88 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8704 (m-10)
REVERT: A   78 PHE cc_start: 0.9402 (t80) cc_final: 0.9161 (t80)
REVERT: A   90 MET cc_start: 0.9099 (mtm) cc_final: 0.8449 (mtm)
REVERT: A   94 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: A  120 MET cc_start: 0.8828 (mmt) cc_final: 0.8176 (mmt)
REVERT: B   63 GLU cc_start: 0.9686 (tp30) cc_final: 0.9390 (tm-30)
  outliers start: 39
  outliers final: 22
  residues processed: 180
  average time/residue: 0.2645
  time to fit residues: 66.0496
Evaluate side-chains
  164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 85 optimal weight:   50.0000
   chunk 28 optimal weight:    2.9990
   chunk 95 optimal weight:   50.0000
   chunk 112 optimal weight:   20.0000
   chunk 90 optimal weight:   50.0000
   chunk 68 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 97 optimal weight:   50.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
D  25 ASN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.047690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.031645 restraints weight = 90891.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.032694 restraints weight = 49084.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.033349 restraints weight = 33746.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11963  Z= 0.286
  Angle     :  0.725  11.572  17123  Z= 0.411
  Chirality :  0.043   0.185   2021
  Planarity :  0.004   0.046   1458
  Dihedral  : 31.689 175.964   3422
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 22.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 33.64 %
    Favored  : 58.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.27), residues: 974
  helix:  0.85 (0.23), residues: 475
  sheet:  0.78 (0.45), residues: 134
  loop : -0.59 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.010   0.002   PHE E  67 
 TYR   0.025   0.002   TYR E  54 
 ARG   0.008   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07355 (  669)
  hydrogen bonds       : angle       4.15997 ( 1689)
  covalent geometry    : bond        0.00622 (11963)
  covalent geometry    : angle       0.72523 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 GLU cc_start: 0.7861 (tt0) cc_final: 0.7257 (mt-10)
REVERT: H   39 ARG cc_start: 0.9048 (mmm-85) cc_final: 0.8570 (mmm-85)
REVERT: H   79 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8796 (pttp)
REVERT: E   64 LYS cc_start: 0.9612 (mmmm) cc_final: 0.9385 (mmmm)
REVERT: F   63 GLU cc_start: 0.8921 (tp30) cc_final: 0.8607 (tp30)
REVERT: F   74 GLU cc_start: 0.8813 (pp20) cc_final: 0.8610 (pp20)
REVERT: F   84 MET cc_start: 0.9329 (tpp) cc_final: 0.8739 (tpp)
REVERT: F   88 TYR cc_start: 0.9460 (m-80) cc_final: 0.8931 (m-80)
REVERT: C   51 ILE cc_start: 0.9123 (mp) cc_final: 0.8878 (mt)
REVERT: C   54 TYR cc_start: 0.9129 (m-80) cc_final: 0.8607 (m-80)
REVERT: C   94 GLU cc_start: 0.9052 (tp30) cc_final: 0.8435 (tp30)
REVERT: C   97 GLU cc_start: 0.8326 (pp20) cc_final: 0.8078 (pp20)
REVERT: C  105 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9177 (mm-30)
REVERT: C  110 CYS cc_start: 0.9737 (m) cc_final: 0.9418 (m)
REVERT: D   25 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8552 (p0)
REVERT: D   53 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8937 (tm-30)
REVERT: D   63 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9105 (mm-30)
REVERT: D   84 MET cc_start: 0.8979 (tpp) cc_final: 0.8431 (tmm)
REVERT: D   85 ASP cc_start: 0.9019 (m-30) cc_final: 0.8644 (t0)
REVERT: A   78 PHE cc_start: 0.9383 (t80) cc_final: 0.9097 (t80)
REVERT: A   90 MET cc_start: 0.9156 (mtm) cc_final: 0.8442 (mtm)
REVERT: A   94 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8681 (mm-30)
REVERT: A  100 LEU cc_start: 0.9785 (tp) cc_final: 0.9510 (tt)
REVERT: A  120 MET cc_start: 0.8674 (mmt) cc_final: 0.8248 (mmt)
REVERT: A  128 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8657 (mmm-85)
REVERT: A  133 GLU cc_start: 0.8541 (mp0) cc_final: 0.8175 (mp0)
REVERT: B   55 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8408 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9620 (tp30) cc_final: 0.9374 (tm-30)
  outliers start: 40
  outliers final: 24
  residues processed: 186
  average time/residue: 0.2621
  time to fit residues: 66.7079
Evaluate side-chains
  166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 91 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
D  25 ASN
** A  76 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.048591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.032884 restraints weight = 86543.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.033982 restraints weight = 46401.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.034683 restraints weight = 31542.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11963  Z= 0.204
  Angle     :  0.703  11.795  17123  Z= 0.394
  Chirality :  0.041   0.235   2021
  Planarity :  0.004   0.029   1458
  Dihedral  : 31.596 175.882   3422
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 19.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 36.43 %
    Favored  : 58.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.27), residues: 974
  helix:  0.86 (0.23), residues: 480
  sheet:  0.60 (0.44), residues: 143
  loop : -0.65 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.013   0.002   PHE E  67 
 TYR   0.017   0.001   TYR F  51 
 ARG   0.005   0.001   ARG G  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06449 (  669)
  hydrogen bonds       : angle       3.95120 ( 1689)
  covalent geometry    : bond        0.00450 (11963)
  covalent geometry    : angle       0.70287 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9668 (tp) cc_final: 0.9104 (mt)
REVERT: G   73 GLU cc_start: 0.7753 (tt0) cc_final: 0.7149 (mt-10)
REVERT: G   97 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8429 (pp20)
REVERT: H   39 ARG cc_start: 0.9037 (mmm-85) cc_final: 0.8603 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9605 (mmmm) cc_final: 0.9381 (mmmm)
REVERT: E  105 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9024 (mm-30)
REVERT: F   63 GLU cc_start: 0.8885 (tp30) cc_final: 0.8621 (tp30)
REVERT: F   74 GLU cc_start: 0.8751 (pp20) cc_final: 0.8538 (pp20)
REVERT: F   84 MET cc_start: 0.9304 (tpp) cc_final: 0.8681 (tpp)
REVERT: F   88 TYR cc_start: 0.9449 (m-80) cc_final: 0.8933 (m-80)
REVERT: C   54 TYR cc_start: 0.8982 (m-80) cc_final: 0.8497 (m-80)
REVERT: C   94 GLU cc_start: 0.9047 (tp30) cc_final: 0.8302 (tp30)
REVERT: C   97 GLU cc_start: 0.8304 (pp20) cc_final: 0.7814 (pp20)
REVERT: C  105 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9315 (mm-30)
REVERT: C  110 CYS cc_start: 0.9723 (m) cc_final: 0.9437 (m)
REVERT: D   25 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8411 (p0)
REVERT: D   26 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9454 (tp)
REVERT: D   63 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9065 (mm-30)
REVERT: D   84 MET cc_start: 0.8894 (tpp) cc_final: 0.8486 (tmm)
REVERT: D   85 ASP cc_start: 0.8975 (m-30) cc_final: 0.8689 (t0)
REVERT: A   78 PHE cc_start: 0.9377 (t80) cc_final: 0.9059 (t80)
REVERT: A   90 MET cc_start: 0.9174 (mtm) cc_final: 0.8727 (mtt)
REVERT: A   94 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8614 (mm-30)
REVERT: A   97 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8972 (pp20)
REVERT: A  120 MET cc_start: 0.8803 (mmt) cc_final: 0.8107 (mmt)
REVERT: B   55 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8613 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9630 (tp30) cc_final: 0.9348 (tm-30)
  outliers start: 29
  outliers final: 21
  residues processed: 174
  average time/residue: 0.2420
  time to fit residues: 58.4304
Evaluate side-chains
  164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 112 optimal weight:   50.0000
   chunk 64 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 60 optimal weight:    9.9990
   chunk 107 optimal weight:   50.0000
   chunk 23 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
G 125 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.047855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.031426 restraints weight = 93937.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.032459 restraints weight = 51650.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.033111 restraints weight = 35980.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11963  Z= 0.249
  Angle     :  0.727  12.536  17123  Z= 0.407
  Chirality :  0.042   0.218   2021
  Planarity :  0.004   0.035   1458
  Dihedral  : 31.726 177.807   3422
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 22.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 37.55 %
    Favored  : 57.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.27), residues: 974
  helix:  0.78 (0.23), residues: 478
  sheet:  0.64 (0.45), residues: 136
  loop : -0.64 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.009   0.002   PHE E  67 
 TYR   0.030   0.002   TYR E  54 
 ARG   0.026   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07073 (  669)
  hydrogen bonds       : angle       4.06631 ( 1689)
  covalent geometry    : bond        0.00549 (11963)
  covalent geometry    : angle       0.72713 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9656 (tp) cc_final: 0.9075 (mt)
REVERT: G   73 GLU cc_start: 0.7707 (tt0) cc_final: 0.7120 (mt-10)
REVERT: G   97 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8483 (pp20)
REVERT: H   39 ARG cc_start: 0.9051 (mmm-85) cc_final: 0.8574 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9618 (mmmm) cc_final: 0.9392 (mmmm)
REVERT: E  105 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9048 (mm-30)
REVERT: F   63 GLU cc_start: 0.8796 (tp30) cc_final: 0.8543 (tp30)
REVERT: F   74 GLU cc_start: 0.8812 (pp20) cc_final: 0.8588 (pp20)
REVERT: F   84 MET cc_start: 0.9295 (tpp) cc_final: 0.8671 (tpp)
REVERT: F   88 TYR cc_start: 0.9468 (m-80) cc_final: 0.8962 (m-80)
REVERT: C   54 TYR cc_start: 0.9035 (m-80) cc_final: 0.8657 (m-80)
REVERT: C   94 GLU cc_start: 0.9088 (tp30) cc_final: 0.8373 (tp30)
REVERT: C   97 GLU cc_start: 0.8337 (pp20) cc_final: 0.7852 (pp20)
REVERT: C  105 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9301 (mm-30)
REVERT: C  110 CYS cc_start: 0.9727 (m) cc_final: 0.9410 (m)
REVERT: D   25 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8218 (p0)
REVERT: D   26 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9520 (tp)
REVERT: D   63 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9084 (mm-30)
REVERT: D   84 MET cc_start: 0.8937 (tpp) cc_final: 0.8453 (tmm)
REVERT: D   85 ASP cc_start: 0.9010 (m-30) cc_final: 0.8661 (t0)
REVERT: D   91 LYS cc_start: 0.9344 (tttp) cc_final: 0.9006 (ttmm)
REVERT: A   78 PHE cc_start: 0.9421 (t80) cc_final: 0.9175 (t80)
REVERT: A   90 MET cc_start: 0.9181 (mtm) cc_final: 0.8756 (mtt)
REVERT: A   94 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8674 (mm-30)
REVERT: A  120 MET cc_start: 0.8821 (mmt) cc_final: 0.8068 (mmt)
REVERT: A  133 GLU cc_start: 0.8756 (mp0) cc_final: 0.8444 (mp0)
REVERT: B   55 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8663 (mtt-85)
REVERT: B   63 GLU cc_start: 0.9640 (tp30) cc_final: 0.9402 (tm-30)
  outliers start: 29
  outliers final: 22
  residues processed: 166
  average time/residue: 0.2500
  time to fit residues: 57.5669
Evaluate side-chains
  161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 87 optimal weight:   50.0000
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 93 optimal weight:    9.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
A  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.049263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.032812 restraints weight = 90630.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.033893 restraints weight = 49569.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.034575 restraints weight = 34261.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.5537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11963  Z= 0.182
  Angle     :  0.723  12.251  17123  Z= 0.397
  Chirality :  0.042   0.351   2021
  Planarity :  0.004   0.059   1458
  Dihedral  : 31.565 176.337   3422
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 18.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 37.36 %
    Favored  : 57.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.27), residues: 974
  helix:  0.82 (0.24), residues: 477
  sheet:  0.68 (0.45), residues: 141
  loop : -0.68 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.017   0.001   PHE A  67 
 TYR   0.009   0.001   TYR C  54 
 ARG   0.015   0.001   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06170 (  669)
  hydrogen bonds       : angle       3.88027 ( 1689)
  covalent geometry    : bond        0.00405 (11963)
  covalent geometry    : angle       0.72320 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9643 (tp) cc_final: 0.9092 (mt)
REVERT: G   73 GLU cc_start: 0.7645 (tt0) cc_final: 0.7065 (mt-10)
REVERT: G   97 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8443 (pp20)
REVERT: G  129 ARG cc_start: 0.9494 (tpp80) cc_final: 0.9263 (ttp80)
REVERT: H   39 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8532 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9605 (mmmm) cc_final: 0.9381 (mmmm)
REVERT: E   68 GLN cc_start: 0.9623 (tt0) cc_final: 0.8957 (tm-30)
REVERT: E  105 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9005 (mm-30)
REVERT: F   63 GLU cc_start: 0.8738 (tp30) cc_final: 0.8422 (tp30)
REVERT: F   74 GLU cc_start: 0.8709 (pp20) cc_final: 0.8454 (pp20)
REVERT: F   84 MET cc_start: 0.9224 (tpp) cc_final: 0.8590 (tpp)
REVERT: F   88 TYR cc_start: 0.9402 (m-80) cc_final: 0.8862 (m-80)
REVERT: C   54 TYR cc_start: 0.9045 (m-80) cc_final: 0.8464 (m-80)
REVERT: C   94 GLU cc_start: 0.9042 (tp30) cc_final: 0.8410 (tp30)
REVERT: C  105 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9282 (mm-30)
REVERT: C  110 CYS cc_start: 0.9728 (m) cc_final: 0.9453 (m)
REVERT: D   25 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8366 (p0)
REVERT: D   26 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9408 (tp)
REVERT: D   63 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9053 (mm-30)
REVERT: D   84 MET cc_start: 0.8913 (tpp) cc_final: 0.8475 (tmm)
REVERT: D   85 ASP cc_start: 0.8913 (m-30) cc_final: 0.8659 (t0)
REVERT: D   91 LYS cc_start: 0.9315 (tttp) cc_final: 0.8985 (ttmm)
REVERT: A   78 PHE cc_start: 0.9407 (t80) cc_final: 0.9169 (t80)
REVERT: A   90 MET cc_start: 0.9175 (mtm) cc_final: 0.8756 (mmm)
REVERT: A   94 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8598 (mm-30)
REVERT: A   97 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8970 (pp20)
REVERT: A  120 MET cc_start: 0.8853 (mmt) cc_final: 0.8410 (mmm)
REVERT: A  133 GLU cc_start: 0.8715 (mp0) cc_final: 0.8368 (mp0)
REVERT: B   55 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8469 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9642 (tp30) cc_final: 0.9390 (tm-30)
  outliers start: 29
  outliers final: 19
  residues processed: 173
  average time/residue: 0.2622
  time to fit residues: 62.2022
Evaluate side-chains
  163 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 97 optimal weight:   50.0000
   chunk 68 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.048541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.032960 restraints weight = 85653.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.033984 restraints weight = 46251.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.034683 restraints weight = 31421.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.5679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  11963  Z= 0.195
  Angle     :  0.743  14.863  17123  Z= 0.407
  Chirality :  0.042   0.380   2021
  Planarity :  0.005   0.106   1458
  Dihedral  : 31.556 177.949   3422
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 38.85 %
    Favored  : 56.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.27), residues: 974
  helix:  0.78 (0.24), residues: 474
  sheet:  0.75 (0.45), residues: 141
  loop : -0.60 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.009   0.001   PHE E 104 
 TYR   0.010   0.001   TYR E  54 
 ARG   0.015   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06287 (  669)
  hydrogen bonds       : angle       3.92105 ( 1689)
  covalent geometry    : bond        0.00435 (11963)
  covalent geometry    : angle       0.74300 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9660 (tp) cc_final: 0.9058 (mt)
REVERT: G   73 GLU cc_start: 0.7721 (tt0) cc_final: 0.7111 (mt-10)
REVERT: H   39 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8522 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9613 (mmmm) cc_final: 0.9389 (mmmm)
REVERT: E   68 GLN cc_start: 0.9649 (tt0) cc_final: 0.8963 (tm-30)
REVERT: E  105 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9023 (mm-30)
REVERT: F   63 GLU cc_start: 0.8697 (tp30) cc_final: 0.8356 (tp30)
REVERT: F   74 GLU cc_start: 0.8700 (pp20) cc_final: 0.8451 (pp20)
REVERT: F   84 MET cc_start: 0.9282 (tpp) cc_final: 0.8662 (tpp)
REVERT: F   88 TYR cc_start: 0.9450 (m-80) cc_final: 0.9003 (m-80)
REVERT: C   94 GLU cc_start: 0.9057 (tp30) cc_final: 0.8834 (tp30)
REVERT: C  105 GLU cc_start: 0.9530 (mm-30) cc_final: 0.9297 (mm-30)
REVERT: C  110 CYS cc_start: 0.9736 (m) cc_final: 0.9459 (m)
REVERT: D   25 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8383 (p0)
REVERT: D   26 ILE cc_start: 0.9636 (OUTLIER) cc_final: 0.9389 (tp)
REVERT: D   63 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9061 (mm-30)
REVERT: D   84 MET cc_start: 0.8896 (tpp) cc_final: 0.8461 (tmm)
REVERT: D   85 ASP cc_start: 0.8944 (m-30) cc_final: 0.8653 (t0)
REVERT: D   91 LYS cc_start: 0.9317 (tttp) cc_final: 0.8992 (ttmm)
REVERT: A   78 PHE cc_start: 0.9384 (t80) cc_final: 0.9164 (t80)
REVERT: A   90 MET cc_start: 0.9162 (mtm) cc_final: 0.8741 (mmm)
REVERT: A   94 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8644 (mm-30)
REVERT: A  120 MET cc_start: 0.8938 (mmt) cc_final: 0.8325 (mmt)
REVERT: A  133 GLU cc_start: 0.8648 (mp0) cc_final: 0.8293 (mp0)
REVERT: B   55 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8429 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9652 (tp30) cc_final: 0.9408 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 167
  average time/residue: 0.2648
  time to fit residues: 60.2902
Evaluate side-chains
  160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:   30.0000
   chunk 55 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 95 optimal weight:    0.0170
   chunk 52 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 102 optimal weight:   50.0000
   chunk 106 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    4.4026

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

Flipped N/Q/H residues before XYZ refinement:
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.046765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.030931 restraints weight = 89092.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.031923 restraints weight = 48952.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.032625 restraints weight = 33661.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.6022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  11963  Z= 0.278
  Angle     :  0.782  14.147  17123  Z= 0.430
  Chirality :  0.044   0.375   2021
  Planarity :  0.005   0.099   1458
  Dihedral  : 31.859 178.331   3422
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 23.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 38.48 %
    Favored  : 56.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.27), residues: 974
  helix:  0.53 (0.23), residues: 473
  sheet:  0.69 (0.45), residues: 139
  loop : -0.57 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.011   0.002   PHE E 104 
 TYR   0.012   0.001   TYR C  99 
 ARG   0.019   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07537 (  669)
  hydrogen bonds       : angle       4.25541 ( 1689)
  covalent geometry    : bond        0.00610 (11963)
  covalent geometry    : angle       0.78158 (17123)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3937.39 seconds
wall clock time: 69 minutes 20.26 seconds (4160.26 seconds total)