Starting phenix.real_space_refine
on Wed Jul 30 16:09:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ck1_16689/07_2025/8ck1_16689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ck1_16689/07_2025/8ck1_16689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ck1_16689/07_2025/8ck1_16689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ck1_16689/07_2025/8ck1_16689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ck1_16689/07_2025/8ck1_16689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ck1_16689/07_2025/8ck1_16689.cif"
  }
  resolution = 3.9
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    7858      2.51       5
     N    2132      2.21       5
     O    2555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12580
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 826, 6419
          Classifications: {'peptide': 826}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 31, 'TRANS': 794}
    Chain: "D"
      Number of atoms: 989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 989
          Classifications: {'peptide': 126}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120}
    Chain: "B"
      Number of atoms: 989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 989
          Classifications: {'peptide': 126}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120}
    Chain: "C"
      Number of atoms: 989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 989
          Classifications: {'peptide': 126}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120}
    Chain: "E"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1597
          Classifications: {'peptide': 206}
          Link IDs: {'PTRANS': 10, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1597
          Classifications: {'peptide': 206}
          Link IDs: {'PTRANS': 10, 'TRANS': 195}
  Time building chain proxies: 7.38, per 1000 atoms: 0.59
  Number of scatterers: 12580
  At special positions: 0
  Unit cell: (89.1, 120.15, 207.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    2555      8.00
     N    2132      7.00
     C    7858      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E   8 " - pdb=" SG  CYS E  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   8 " - pdb=" SG  CYS F  34 " distance=2.04

  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: 3.26
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2966

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 26 sheets defined
      22.4% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 29
      removed outlier: 4.257A  pdb=" N   GLY A  28 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 37
      removed outlier: 3.766A  pdb=" N   ALA A  36 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 82
      No H-bonds generated for 'chain 'A' and resid 80 through 82'
    Processing helix  chain 'A' and resid 120 through 124
    Processing helix  chain 'A' and resid 310 through 316
      removed outlier: 4.079A  pdb=" N   ARG A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 479
    Processing helix  chain 'A' and resid 512 through 516
    Processing helix  chain 'A' and resid 552 through 555
    Processing helix  chain 'A' and resid 570 through 574
    Processing helix  chain 'A' and resid 617 through 621
    Processing helix  chain 'A' and resid 656 through 660
    Processing helix  chain 'A' and resid 677 through 681
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.534A  pdb=" N   LEU A 769 " --> pdb=" O   SER A 766 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 127
      removed outlier: 4.056A  pdb=" N   VAL D 106 " --> pdb=" O   TYR D 102 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG D 126 " --> pdb=" O   GLU D 122 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ALA D 127 " --> pdb=" O   GLN D 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 127
      removed outlier: 3.798A  pdb=" N   VAL B 106 " --> pdb=" O   TYR B 102 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG B 126 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA B 127 " --> pdb=" O   GLN B 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 31
      No H-bonds generated for 'chain 'C' and resid 29 through 31'
    Processing helix  chain 'C' and resid 48 through 52
    Processing helix  chain 'C' and resid 102 through 127
      removed outlier: 3.511A  pdb=" N   VAL C 106 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA C 127 " --> pdb=" O   GLN C 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 16
      removed outlier: 3.693A  pdb=" N   GLY E  16 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 49
      removed outlier: 3.507A  pdb=" N   ARG E  32 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ALA E  40 " --> pdb=" O   GLN E  36 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG E  47 " --> pdb=" O   ALA E  43 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 53
      No H-bonds generated for 'chain 'E' and resid 51 through 53'
    Processing helix  chain 'E' and resid 95 through 99
    Processing helix  chain 'E' and resid 137 through 141
    Processing helix  chain 'E' and resid 142 through 163
      removed outlier: 4.871A  pdb=" N   MET E 159 " --> pdb=" O   LYS E 155 " (cutoff:3.500A)
      Proline residue:  E 160  - end of helix
    Processing helix  chain 'E' and resid 164 through 189
    Processing helix  chain 'E' and resid 198 through 203
    Processing helix  chain 'F' and resid 3 through 16
    Processing helix  chain 'F' and resid 20 through 24
    Processing helix  chain 'F' and resid 28 through 49
      removed outlier: 4.215A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 95 through 99
      removed outlier: 3.569A  pdb=" N   GLU F  98 " --> pdb=" O   GLY F  95 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE F  99 " --> pdb=" O   ALA F  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 95 through 99'
    Processing helix  chain 'F' and resid 142 through 163
      removed outlier: 4.628A  pdb=" N   MET F 159 " --> pdb=" O   LYS F 155 " (cutoff:3.500A)
      Proline residue:  F 160  - end of helix
    Processing helix  chain 'F' and resid 164 through 189
    Processing helix  chain 'F' and resid 198 through 206
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43
      removed outlier: 3.650A  pdb=" N   SER A 721 " --> pdb=" O   GLN A 809 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47
    Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 64
      removed outlier: 5.675A  pdb=" N   PHE A  61 " --> pdb=" O   TYR A 562 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   TYR A 562 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   THR A  63 " --> pdb=" O   ILE A 560 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A 543 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A 536 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER A 532 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   LYS A 549 " --> pdb=" O   PHE A 530 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   PHE A 530 " --> pdb=" O   LYS A 549 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 78
      removed outlier: 3.691A  pdb=" N   GLY A  90 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR A  93 " --> pdb=" O   GLY A  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 98
    Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 129
      removed outlier: 6.005A  pdb=" N   HIS A 137 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   LYS A 141 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   LEU A 145 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ASP A 156 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   ARG A 147 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL A 154 " --> pdb=" O   ARG A 147 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 178
      removed outlier: 3.784A  pdb=" N   ILE A 301 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   HIS A 300 " --> pdb=" O   HIS A 295 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   HIS A 295 " --> pdb=" O   HIS A 300 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   VAL A 302 " --> pdb=" O   THR A 293 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 205 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ARG A 320 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 235 through 236
    Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 339
    Processing sheet with id=AB1, first strand: chain 'A' and resid 390 through 395
      removed outlier: 3.642A  pdb=" N   LEU A 399 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 438 through 440
    Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 500
    Processing sheet with id=AB4, first strand: chain 'A' and resid 578 through 582
      removed outlier: 4.416A  pdb=" N   GLY A 580 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL A 715 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   THR A 582 " --> pdb=" O   VAL A 713 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   VAL A 713 " --> pdb=" O   THR A 582 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ILE A 687 " --> pdb=" O   HIS A 694 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 596
      removed outlier: 7.452A  pdb=" N   ALA A 648 " --> pdb=" O   ASP A 639 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ARG A 666 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 671 through 674
      removed outlier: 6.189A  pdb=" N   LYS A 672 " --> pdb=" O   LEU A 706 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 792 through 794
      removed outlier: 5.555A  pdb=" N   ILE A 742 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL A 825 " --> pdb=" O   ILE A 742 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLY A 744 " --> pdb=" O   ARG A 823 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 749 through 752
      removed outlier: 6.001A  pdb=" N   GLU A 787 " --> pdb=" O   LYS A 751 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 13
    Processing sheet with id=AC1, first strand: chain 'D' and resid 55 through 56
    Processing sheet with id=AC2, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AC3, first strand: chain 'B' and resid 20 through 23
    Processing sheet with id=AC4, first strand: chain 'C' and resid 9 through 12
      removed outlier: 3.929A  pdb=" N   THR C  82 " --> pdb=" O   TYR C  36 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 55 through 59
      removed outlier: 3.649A  pdb=" N   ASP E  85 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   THR E 132 " --> pdb=" O   ILE E  83 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE E  83 " --> pdb=" O   THR E 132 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 61 through 64
      removed outlier: 4.615A  pdb=" N   ALA E  61 " --> pdb=" O   ARG E  75 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LYS E  73 " --> pdb=" O   ILE E  63 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA E 122 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 55 through 59
      removed outlier: 3.766A  pdb=" N   ASP F  85 " --> pdb=" O   ARG F 130 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   THR F 132 " --> pdb=" O   ILE F  83 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE F  83 " --> pdb=" O   THR F 132 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 62 through 64
      removed outlier: 7.216A  pdb=" N   LYS F  73 " --> pdb=" O   ILE F  63 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1089 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.80

  Time building geometry restraints manager: 3.89 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4241
        1.34 -     1.46: 3037
        1.46 -     1.59: 5499
        1.59 -     1.72: 0
        1.72 -     1.85: 59
  Bond restraints: 12836
  Sorted by residual:
  bond pdb=" C   VAL A  47 "
       pdb=" N   GLN A  48 "
    ideal  model  delta    sigma   weight residual
    1.333  1.403 -0.070 1.39e-02 5.18e+03 2.56e+01
  bond pdb=" C   GLN A  48 "
       pdb=" N   PRO A  49 "
    ideal  model  delta    sigma   weight residual
    1.334  1.425 -0.091 2.34e-02 1.83e+03 1.52e+01
  bond pdb=" N   ILE D  87 "
       pdb=" CA  ILE D  87 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   VAL A  46 "
       pdb=" CA  VAL A  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.17e-02 7.31e+03 8.47e+00
  bond pdb=" N   ILE A 410 "
       pdb=" CA  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.21e-02 6.83e+03 7.96e+00
  ... (remaining 12831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 16921
        1.99 -     3.98: 483
        3.98 -     5.96: 55
        5.96 -     7.95: 9
        7.95 -     9.94: 3
  Bond angle restraints: 17471
  Sorted by residual:
  angle pdb=" O   VAL A  47 "
        pdb=" C   VAL A  47 "
        pdb=" N   GLN A  48 "
      ideal   model   delta    sigma   weight residual
     122.57  127.86   -5.29 1.25e+00 6.40e-01 1.79e+01
  angle pdb=" C   TYR E  38 "
        pdb=" N   ASP E  39 "
        pdb=" CA  ASP E  39 "
      ideal   model   delta    sigma   weight residual
     120.44  115.56    4.88 1.30e+00 5.92e-01 1.41e+01
  angle pdb=" C   GLY C  59 "
        pdb=" N   ASP C  60 "
        pdb=" CA  ASP C  60 "
      ideal   model   delta    sigma   weight residual
     121.54  128.54   -7.00 1.91e+00 2.74e-01 1.34e+01
  angle pdb=" N   THR D  51 "
        pdb=" CA  THR D  51 "
        pdb=" C   THR D  51 "
      ideal   model   delta    sigma   weight residual
     113.43  108.91    4.52 1.26e+00 6.30e-01 1.29e+01
  angle pdb=" N   LEU B  95 "
        pdb=" CA  LEU B  95 "
        pdb=" C   LEU B  95 "
      ideal   model   delta    sigma   weight residual
     114.56  110.02    4.54 1.27e+00 6.20e-01 1.28e+01
  ... (remaining 17466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6579
       17.85 -    35.71: 784
       35.71 -    53.56: 200
       53.56 -    71.41: 37
       71.41 -    89.26: 19
  Dihedral angle restraints: 7619
    sinusoidal: 2974
      harmonic: 4645
  Sorted by residual:
  dihedral pdb=" CA  ALA A 777 "
           pdb=" C   ALA A 777 "
           pdb=" N   GLU A 778 "
           pdb=" CA  GLU A 778 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.86   20.14     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  TRP A 408 "
           pdb=" C   TRP A 408 "
           pdb=" N   MET A 409 "
           pdb=" CA  MET A 409 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.40   19.60     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ASP C  73 "
           pdb=" C   ASP C  73 "
           pdb=" N   PRO C  74 "
           pdb=" CA  PRO C  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.86   18.14     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 7616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1389
       0.044 -    0.087: 367
       0.087 -    0.131: 160
       0.131 -    0.174: 18
       0.174 -    0.218: 6
  Chirality restraints: 1940
  Sorted by residual:
  chirality pdb=" CA  LEU A 659 "
            pdb=" N   LEU A 659 "
            pdb=" C   LEU A 659 "
            pdb=" CB  LEU A 659 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  ILE E 107 "
            pdb=" N   ILE E 107 "
            pdb=" C   ILE E 107 "
            pdb=" CB  ILE E 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE E 205 "
            pdb=" N   ILE E 205 "
            pdb=" C   ILE E 205 "
            pdb=" CB  ILE E 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.51e-01
  ... (remaining 1937 not shown)

  Planarity restraints: 2322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F 203 "    0.017 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   ALA F 203 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   ALA F 203 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN F 204 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 102 "    0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO D 103 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 104 "    0.016 2.00e-02 2.50e+03   1.50e-02 4.53e+00
        pdb=" CG  TYR F 104 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 104 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 104 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 104 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 104 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 104 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR F 104 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2319 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2536
        2.77 -     3.30: 12767
        3.30 -     3.83: 21314
        3.83 -     4.37: 24700
        4.37 -     4.90: 41815
  Nonbonded interactions: 103132
  Sorted by model distance:
  nonbonded pdb=" O   ASP F 207 "
            pdb=" OD1 ASP F 207 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OH  TYR B  12 "
            pdb=" O   PRO B  22 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG  SER A 384 "
            pdb=" N   ARG A 385 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   GLU E  98 "
            pdb=" ND2 ASN E 193 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   GLY A 590 "
            pdb=" OG  SER A 612 "
     model   vdw
     2.267 3.040
  ... (remaining 103127 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 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     32.180
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
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   0.091  12838  Z= 0.243
  Angle     :  0.752   9.938  17475  Z= 0.445
  Chirality :  0.047   0.218   1940
  Planarity :  0.004   0.062   2322
  Dihedral  : 16.949  89.264   4647
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 26.21 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -2.07 (0.21), residues: 1604
  helix:  0.51 (0.32), residues: 278
  sheet: -1.80 (0.25), residues: 419
  loop : -1.78 (0.20), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP F  37 
 HIS   0.005   0.001   HIS F  84 
 PHE   0.015   0.002   PHE F  53 
 TYR   0.037   0.002   TYR F 104 
 ARG   0.004   0.000   ARG F  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21862 (  429)
  hydrogen bonds       : angle       8.74618 ( 1089)
  SS BOND              : bond        0.00427 (    2)
  SS BOND              : angle       3.95646 (    4)
  covalent geometry    : bond        0.00422 (12836)
  covalent geometry    : angle       0.74944 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 326
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8105 (m-80)
REVERT: A  492 GLU cc_start: 0.7998 (tp30) cc_final: 0.6683 (mt-10)
REVERT: A  631 ASP cc_start: 0.7167 (m-30) cc_final: 0.6700 (t0)
REVERT: D   62 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7338 (tm-30)
REVERT: D   68 PHE cc_start: 0.5675 (t80) cc_final: 0.5286 (t80)
REVERT: B   67 THR cc_start: 0.8754 (m) cc_final: 0.8500 (t)
REVERT: C   92 GLU cc_start: 0.7751 (mp0) cc_final: 0.7535 (mp0)
REVERT: C  112 ARG cc_start: 0.8921 (mmt180) cc_final: 0.8533 (mmt180)
REVERT: E   27 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7258 (mtpt)
REVERT: E   79 ASP cc_start: 0.7581 (p0) cc_final: 0.7338 (p0)
REVERT: E   94 ASP cc_start: 0.7228 (t70) cc_final: 0.6789 (t70)
REVERT: E  144 ASP cc_start: 0.8980 (p0) cc_final: 0.8724 (p0)
REVERT: E  204 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7233 (t0)
REVERT: F   18 ASP cc_start: 0.8619 (t0) cc_final: 0.8272 (p0)
  outliers start: 8
  outliers final: 2
  residues processed: 328
  average time/residue: 0.3126
  time to fit residues: 148.1388
Evaluate side-chains
  274 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 270
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue  660 ARG
Chi-restraints excluded: chain E residue   92 TYR
Chi-restraints excluded: chain E residue  204 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    6.9990
   chunk 119 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 123 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 143 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 169 ASN
A 353 GLN
D   6 ASN
D  98 GLN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 GLN
C 120 GLN
F  14 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.096773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.086015 restraints weight = 35335.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.088137 restraints weight = 16811.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.089491 restraints weight = 9603.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12838  Z= 0.211
  Angle     :  0.629   8.597  17475  Z= 0.334
  Chirality :  0.046   0.193   1940
  Planarity :  0.005   0.055   2322
  Dihedral  :  5.098  50.949   1787
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 25.46 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.93 (0.21), residues: 1604
  helix:  0.82 (0.30), residues: 287
  sheet: -1.72 (0.25), residues: 432
  loop : -1.78 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F  37 
 HIS   0.004   0.001   HIS F  84 
 PHE   0.015   0.002   PHE D  21 
 TYR   0.024   0.002   TYR A 482 
 ARG   0.004   0.001   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04878 (  429)
  hydrogen bonds       : angle       6.42202 ( 1089)
  SS BOND              : bond        0.00430 (    2)
  SS BOND              : angle       2.53899 (    4)
  covalent geometry    : bond        0.00472 (12836)
  covalent geometry    : angle       0.62794 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 273
  time to evaluate  : 2.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8406 (p)
REVERT: A  487 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.7415 (m-10)
REVERT: A  492 GLU cc_start: 0.8173 (tp30) cc_final: 0.7060 (mt-10)
REVERT: D  111 ASP cc_start: 0.8356 (m-30) cc_final: 0.8143 (m-30)
REVERT: B   67 THR cc_start: 0.8681 (m) cc_final: 0.8284 (t)
REVERT: B  110 PHE cc_start: 0.8088 (t80) cc_final: 0.7836 (t80)
REVERT: B  120 GLN cc_start: 0.8573 (mt0) cc_final: 0.8107 (mt0)
REVERT: C   81 LEU cc_start: 0.6026 (tp) cc_final: 0.5759 (mm)
REVERT: C   98 GLN cc_start: 0.8636 (mp10) cc_final: 0.8392 (mp10)
REVERT: C  101 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7851 (m-80)
REVERT: C  112 ARG cc_start: 0.8932 (mmt180) cc_final: 0.8441 (mmt180)
REVERT: C  119 GLN cc_start: 0.8556 (mt0) cc_final: 0.8072 (mp10)
REVERT: E   14 ASN cc_start: 0.9082 (t0) cc_final: 0.8774 (t0)
REVERT: E   27 LYS cc_start: 0.8465 (mtmm) cc_final: 0.7668 (mtpt)
REVERT: E   79 ASP cc_start: 0.7962 (p0) cc_final: 0.7612 (p0)
REVERT: E   94 ASP cc_start: 0.7185 (t0) cc_final: 0.6867 (t70)
REVERT: E  144 ASP cc_start: 0.9018 (p0) cc_final: 0.8653 (p0)
REVERT: E  151 MET cc_start: 0.9220 (mmm) cc_final: 0.8903 (tpt)
REVERT: F    4 LYS cc_start: 0.6220 (tmtt) cc_final: 0.5531 (tptp)
REVERT: F    9 ASN cc_start: 0.7944 (m-40) cc_final: 0.7618 (m110)
REVERT: F   18 ASP cc_start: 0.8756 (t0) cc_final: 0.8422 (p0)
REVERT: F  131 TYR cc_start: 0.7780 (p90) cc_final: 0.7254 (p90)
REVERT: F  141 MET cc_start: 0.8787 (pmm) cc_final: 0.8469 (pmm)
  outliers start: 62
  outliers final: 34
  residues processed: 310
  average time/residue: 0.2957
  time to fit residues: 137.5058
Evaluate side-chains
  289 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 252
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  353 GLN
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  170 VAL
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  191 TYR
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 143 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 147 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 139 optimal weight:   10.0000
   overall best weight:    4.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 427 GLN
A 774 GLN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 173 GLN
F  14 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  84 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.086117 restraints weight = 35801.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.088261 restraints weight = 17035.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.089625 restraints weight = 9722.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12838  Z= 0.180
  Angle     :  0.594  10.000  17475  Z= 0.312
  Chirality :  0.045   0.206   1940
  Planarity :  0.004   0.048   2322
  Dihedral  :  4.614  20.508   1777
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.58 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.75 (0.21), residues: 1604
  helix:  1.14 (0.30), residues: 290
  sheet: -1.45 (0.26), residues: 404
  loop : -1.84 (0.20), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F  37 
 HIS   0.004   0.001   HIS F  84 
 PHE   0.014   0.001   PHE F  53 
 TYR   0.022   0.002   TYR C 101 
 ARG   0.004   0.000   ARG A 660 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04372 (  429)
  hydrogen bonds       : angle       5.92001 ( 1089)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       1.86716 (    4)
  covalent geometry    : bond        0.00404 (12836)
  covalent geometry    : angle       0.59324 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 268
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8562 (m-80)
REVERT: A   54 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8445 (p)
REVERT: A  343 LEU cc_start: 0.8691 (tp) cc_final: 0.8468 (tp)
REVERT: A  487 TRP cc_start: 0.8692 (OUTLIER) cc_final: 0.7474 (m-10)
REVERT: A  492 GLU cc_start: 0.8059 (tp30) cc_final: 0.7049 (mt-10)
REVERT: A  670 MET cc_start: 0.7656 (mtm) cc_final: 0.7198 (mtm)
REVERT: D   62 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7360 (tm-30)
REVERT: D  121 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: B    9 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7925 (ttm-80)
REVERT: B   67 THR cc_start: 0.8697 (m) cc_final: 0.8322 (t)
REVERT: B   87 ILE cc_start: 0.9156 (tp) cc_final: 0.8901 (tp)
REVERT: B   89 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7427 (mm)
REVERT: B   98 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7911 (mm-40)
REVERT: B  120 GLN cc_start: 0.8266 (mt0) cc_final: 0.7535 (mt0)
REVERT: C    6 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7874 (t0)
REVERT: C  101 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7763 (m-80)
REVERT: C  119 GLN cc_start: 0.8457 (mt0) cc_final: 0.8240 (mp10)
REVERT: E   27 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7759 (mtpt)
REVERT: E   79 ASP cc_start: 0.7924 (p0) cc_final: 0.7522 (p0)
REVERT: E  144 ASP cc_start: 0.8992 (p0) cc_final: 0.8587 (p0)
REVERT: E  151 MET cc_start: 0.9225 (mmm) cc_final: 0.8911 (tpt)
REVERT: F    3 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8616 (p)
REVERT: F    9 ASN cc_start: 0.8000 (m-40) cc_final: 0.7719 (m110)
REVERT: F   18 ASP cc_start: 0.8734 (t0) cc_final: 0.8432 (p0)
REVERT: F   32 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7311 (mtt-85)
REVERT: F  131 TYR cc_start: 0.7971 (p90) cc_final: 0.7382 (p90)
REVERT: F  141 MET cc_start: 0.8768 (pmm) cc_final: 0.8561 (pmm)
REVERT: F  159 MET cc_start: 0.8065 (tpp) cc_final: 0.7843 (mmt)
  outliers start: 58
  outliers final: 37
  residues processed: 310
  average time/residue: 0.3520
  time to fit residues: 164.7217
Evaluate side-chains
  298 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 252
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  820 ILE
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain F residue    3 SER
Chi-restraints excluded: chain F residue   32 ARG
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 117 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 116 optimal weight:    4.9990
   chunk 79 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0980
   chunk 48 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0040
   chunk 71 optimal weight:    8.9990
   overall best weight:    3.8198

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

Flipped N/Q/H residues before XYZ refinement:
** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 173 GLN
F  14 ASN
** F  36 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 = 0.3331 r_free = 0.3331 target = 0.097370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.086376 restraints weight = 35350.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.088517 restraints weight = 16802.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.089882 restraints weight = 9615.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12838  Z= 0.168
  Angle     :  0.581  10.443  17475  Z= 0.305
  Chirality :  0.044   0.211   1940
  Planarity :  0.004   0.043   2322
  Dihedral  :  4.542  20.104   1777
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 26.73 %
    Favored  : 68.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.67 (0.21), residues: 1604
  helix:  1.34 (0.30), residues: 290
  sheet: -1.45 (0.25), residues: 412
  loop : -1.81 (0.20), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 216 
 HIS   0.004   0.001   HIS F  84 
 PHE   0.021   0.001   PHE B  21 
 TYR   0.022   0.002   TYR C  53 
 ARG   0.004   0.000   ARG C   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04144 (  429)
  hydrogen bonds       : angle       5.66210 ( 1089)
  SS BOND              : bond        0.00338 (    2)
  SS BOND              : angle       1.67139 (    4)
  covalent geometry    : bond        0.00383 (12836)
  covalent geometry    : angle       0.58026 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 263
  time to evaluate  : 1.638 
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: A   45 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8604 (m-80)
REVERT: A   54 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8420 (p)
REVERT: A  212 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7960 (tp30)
REVERT: A  487 TRP cc_start: 0.8649 (OUTLIER) cc_final: 0.7411 (m-10)
REVERT: A  492 GLU cc_start: 0.7737 (tp30) cc_final: 0.6817 (mt-10)
REVERT: D   62 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7659 (tm-30)
REVERT: D  121 GLN cc_start: 0.8285 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: B    9 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8020 (ttm-80)
REVERT: B   67 THR cc_start: 0.8715 (m) cc_final: 0.8326 (t)
REVERT: B   87 ILE cc_start: 0.9154 (tp) cc_final: 0.8902 (tp)
REVERT: B   92 GLU cc_start: 0.7538 (tp30) cc_final: 0.7337 (tp30)
REVERT: B   98 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7877 (mm-40)
REVERT: B  120 GLN cc_start: 0.8303 (mt0) cc_final: 0.7604 (mt0)
REVERT: C    9 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7408 (ttp80)
REVERT: C   11 GLN cc_start: 0.7707 (tp40) cc_final: 0.7327 (mp10)
REVERT: C   48 ILE cc_start: 0.9072 (mm) cc_final: 0.8846 (mt)
REVERT: C  101 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7715 (m-80)
REVERT: E   79 ASP cc_start: 0.7931 (p0) cc_final: 0.7588 (p0)
REVERT: E  144 ASP cc_start: 0.8981 (p0) cc_final: 0.8588 (p0)
REVERT: E  151 MET cc_start: 0.9083 (mmm) cc_final: 0.8882 (tpt)
REVERT: E  205 ILE cc_start: 0.8413 (tp) cc_final: 0.8198 (tp)
REVERT: F   18 ASP cc_start: 0.8758 (t0) cc_final: 0.8419 (p0)
REVERT: F   32 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7316 (mtt-85)
REVERT: F  131 TYR cc_start: 0.7922 (p90) cc_final: 0.7253 (p90)
  outliers start: 71
  outliers final: 50
  residues processed: 313
  average time/residue: 0.3252
  time to fit residues: 151.7242
Evaluate side-chains
  306 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 249
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue   14 ASN
Chi-restraints excluded: chain F residue   32 ARG
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  132 THR
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  191 TYR
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 133 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 135 optimal weight:    8.9990
   chunk 85 optimal weight:   30.0000
   chunk 73 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 ASN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN
E 173 GLN
F  14 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.096184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.085104 restraints weight = 35838.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.087237 restraints weight = 17150.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.088589 restraints weight = 9864.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12838  Z= 0.210
  Angle     :  0.603  10.428  17475  Z= 0.317
  Chirality :  0.045   0.215   1940
  Planarity :  0.004   0.042   2322
  Dihedral  :  4.672  20.257   1777
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 26.21 %
    Favored  : 67.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.66 (0.21), residues: 1604
  helix:  1.27 (0.30), residues: 290
  sheet: -1.41 (0.26), residues: 407
  loop : -1.80 (0.20), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 216 
 HIS   0.005   0.001   HIS F  84 
 PHE   0.014   0.002   PHE B  21 
 TYR   0.023   0.002   TYR C 101 
 ARG   0.003   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  429)
  hydrogen bonds       : angle       5.71316 ( 1089)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       1.77528 (    4)
  covalent geometry    : bond        0.00474 (12836)
  covalent geometry    : angle       0.60231 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 268
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8715 (m-80)
REVERT: A   54 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8433 (p)
REVERT: A  199 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8769 (t)
REVERT: A  212 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8126 (tp30)
REVERT: A  487 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.7550 (m-10)
REVERT: A  492 GLU cc_start: 0.7838 (tp30) cc_final: 0.6840 (mt-10)
REVERT: A  670 MET cc_start: 0.7676 (mtm) cc_final: 0.6904 (mpp)
REVERT: D   62 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: D   82 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7833 (p)
REVERT: D  121 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: B    9 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8135 (ttm-80)
REVERT: B   67 THR cc_start: 0.8593 (m) cc_final: 0.8191 (t)
REVERT: B   87 ILE cc_start: 0.9181 (tp) cc_final: 0.8934 (tp)
REVERT: B   92 GLU cc_start: 0.7590 (tp30) cc_final: 0.7273 (tp30)
REVERT: B   98 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7846 (mm-40)
REVERT: B  107 GLU cc_start: 0.8023 (tp30) cc_final: 0.7635 (tp30)
REVERT: B  120 GLN cc_start: 0.8240 (mt0) cc_final: 0.7469 (mt0)
REVERT: C    9 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7504 (ttp80)
REVERT: C   11 GLN cc_start: 0.7662 (tp40) cc_final: 0.7308 (mp10)
REVERT: C   48 ILE cc_start: 0.9093 (mm) cc_final: 0.8864 (mt)
REVERT: C   91 GLN cc_start: 0.7855 (tt0) cc_final: 0.7530 (pt0)
REVERT: C  101 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7865 (m-80)
REVERT: E   79 ASP cc_start: 0.7956 (p0) cc_final: 0.7626 (p0)
REVERT: E  144 ASP cc_start: 0.8951 (p0) cc_final: 0.8581 (p0)
REVERT: E  161 MET cc_start: 0.8475 (tmm) cc_final: 0.8141 (tmm)
REVERT: F    3 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (p)
REVERT: F    9 ASN cc_start: 0.8072 (m-40) cc_final: 0.7798 (m110)
REVERT: F   18 ASP cc_start: 0.8806 (t0) cc_final: 0.8426 (p0)
REVERT: F   32 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7329 (mtt-85)
REVERT: F  131 TYR cc_start: 0.7933 (p90) cc_final: 0.7231 (p90)
  outliers start: 84
  outliers final: 56
  residues processed: 324
  average time/residue: 0.2996
  time to fit residues: 146.7857
Evaluate side-chains
  320 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 254
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   82 THR
Chi-restraints excluded: chain B residue    2 THR
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    3 SER
Chi-restraints excluded: chain F residue   32 ARG
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  132 THR
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 107 optimal weight:   20.0000
   chunk 137 optimal weight:   10.0000
   chunk 59 optimal weight:   30.0000
   chunk 113 optimal weight:    7.9990
   chunk 9 optimal weight:    0.2980
   chunk 121 optimal weight:    7.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 GLN
D  98 GLN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 173 GLN
F  14 ASN
F  36 GLN
** F  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.097652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.086656 restraints weight = 36054.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.088803 restraints weight = 17132.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.090156 restraints weight = 9789.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12838  Z= 0.168
  Angle     :  0.587  10.187  17475  Z= 0.308
  Chirality :  0.044   0.221   1940
  Planarity :  0.004   0.039   2322
  Dihedral  :  4.566  19.974   1777
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 27.91 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.62 (0.21), residues: 1604
  helix:  1.33 (0.30), residues: 290
  sheet: -1.41 (0.25), residues: 418
  loop : -1.76 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F  37 
 HIS   0.004   0.001   HIS F  84 
 PHE   0.014   0.001   PHE B 110 
 TYR   0.024   0.002   TYR C  53 
 ARG   0.003   0.000   ARG D  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  429)
  hydrogen bonds       : angle       5.55220 ( 1089)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       1.71058 (    4)
  covalent geometry    : bond        0.00384 (12836)
  covalent geometry    : angle       0.58663 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 264
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8687 (m-80)
REVERT: A  199 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8787 (t)
REVERT: A  343 LEU cc_start: 0.8686 (tp) cc_final: 0.8426 (tp)
REVERT: A  487 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.7364 (m-10)
REVERT: A  492 GLU cc_start: 0.7575 (tp30) cc_final: 0.6831 (mt-10)
REVERT: A  670 MET cc_start: 0.7618 (mtm) cc_final: 0.7090 (mtm)
REVERT: D   62 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: D  121 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: B    9 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8312 (ttm-80)
REVERT: B   67 THR cc_start: 0.8531 (m) cc_final: 0.8125 (t)
REVERT: B   87 ILE cc_start: 0.9166 (tp) cc_final: 0.8906 (tp)
REVERT: B   92 GLU cc_start: 0.7492 (tp30) cc_final: 0.7159 (tp30)
REVERT: B   98 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7960 (mm-40)
REVERT: B  107 GLU cc_start: 0.8001 (tp30) cc_final: 0.7582 (tp30)
REVERT: B  120 GLN cc_start: 0.8243 (mt0) cc_final: 0.7507 (mt0)
REVERT: C    9 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7560 (ttp80)
REVERT: C   48 ILE cc_start: 0.9074 (mm) cc_final: 0.8839 (mt)
REVERT: C  101 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7819 (m-80)
REVERT: E   38 TYR cc_start: 0.8701 (t80) cc_final: 0.8260 (t80)
REVERT: E   79 ASP cc_start: 0.7941 (p0) cc_final: 0.7604 (p0)
REVERT: E  137 ASP cc_start: 0.8358 (t0) cc_final: 0.8139 (t0)
REVERT: E  144 ASP cc_start: 0.8911 (p0) cc_final: 0.8524 (p0)
REVERT: E  151 MET cc_start: 0.8766 (tpt) cc_final: 0.8521 (tpp)
REVERT: E  159 MET cc_start: 0.8601 (tpt) cc_final: 0.7556 (tmm)
REVERT: E  161 MET cc_start: 0.8587 (tmm) cc_final: 0.8194 (tmm)
REVERT: F    3 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8420 (p)
REVERT: F   18 ASP cc_start: 0.8724 (t0) cc_final: 0.8377 (p0)
REVERT: F  131 TYR cc_start: 0.7964 (p90) cc_final: 0.7205 (p90)
  outliers start: 75
  outliers final: 55
  residues processed: 320
  average time/residue: 0.2512
  time to fit residues: 117.5118
Evaluate side-chains
  321 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 260
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 SER
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain B residue    2 THR
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    3 SER
Chi-restraints excluded: chain F residue   14 ASN
Chi-restraints excluded: chain F residue   36 GLN
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  141 MET
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Chi-restraints excluded: chain F residue  207 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 140 optimal weight:    0.9990
   chunk 83 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 77 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
B   8 ASN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 120 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  14 ASN
F  36 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.095331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.084514 restraints weight = 36028.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.086618 restraints weight = 17257.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.087955 restraints weight = 9921.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  12838  Z= 0.286
  Angle     :  0.687   9.910  17475  Z= 0.362
  Chirality :  0.047   0.217   1940
  Planarity :  0.005   0.041   2322
  Dihedral  :  4.934  20.744   1777
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 26.43 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.86 (0.20), residues: 1604
  helix:  0.95 (0.29), residues: 296
  sheet: -1.55 (0.25), residues: 412
  loop : -1.88 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 216 
 HIS   0.006   0.001   HIS F  84 
 PHE   0.020   0.002   PHE B 110 
 TYR   0.023   0.002   TYR C 101 
 ARG   0.005   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04678 (  429)
  hydrogen bonds       : angle       5.84452 ( 1089)
  SS BOND              : bond        0.00656 (    2)
  SS BOND              : angle       4.32382 (    4)
  covalent geometry    : bond        0.00644 (12836)
  covalent geometry    : angle       0.68441 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 260
  time to evaluate  : 2.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8470 (p)
REVERT: A  199 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8687 (t)
REVERT: A  487 TRP cc_start: 0.8742 (OUTLIER) cc_final: 0.7438 (m-10)
REVERT: A  492 GLU cc_start: 0.7683 (tp30) cc_final: 0.7020 (mt-10)
REVERT: A  670 MET cc_start: 0.7612 (mtm) cc_final: 0.7242 (mtm)
REVERT: A  750 GLU cc_start: 0.6151 (tp30) cc_final: 0.5840 (tp30)
REVERT: D   62 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: B    6 ASN cc_start: 0.7434 (t0) cc_final: 0.7215 (t0)
REVERT: B    9 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8328 (ttm-80)
REVERT: B   67 THR cc_start: 0.8627 (m) cc_final: 0.8216 (t)
REVERT: B   92 GLU cc_start: 0.7608 (tp30) cc_final: 0.7222 (tp30)
REVERT: B   98 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7999 (mm-40)
REVERT: B  107 GLU cc_start: 0.8045 (tp30) cc_final: 0.7519 (tp30)
REVERT: B  120 GLN cc_start: 0.8212 (mt0) cc_final: 0.7482 (mt0)
REVERT: C   11 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7584 (mp10)
REVERT: C   48 ILE cc_start: 0.9112 (mm) cc_final: 0.8455 (mt)
REVERT: C  101 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7941 (m-80)
REVERT: C  112 ARG cc_start: 0.8973 (mmt180) cc_final: 0.8440 (mmt180)
REVERT: E   79 ASP cc_start: 0.7876 (p0) cc_final: 0.7603 (p0)
REVERT: E  137 ASP cc_start: 0.8407 (t0) cc_final: 0.8176 (t0)
REVERT: E  144 ASP cc_start: 0.8953 (p0) cc_final: 0.8574 (p0)
REVERT: E  151 MET cc_start: 0.8696 (tpt) cc_final: 0.8476 (tpp)
REVERT: E  161 MET cc_start: 0.8619 (tmm) cc_final: 0.8331 (tmm)
REVERT: F    9 ASN cc_start: 0.8199 (m-40) cc_final: 0.7968 (m110)
REVERT: F   18 ASP cc_start: 0.8837 (t0) cc_final: 0.8411 (p0)
REVERT: F   28 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7558 (m)
REVERT: F   30 GLU cc_start: 0.8491 (mp0) cc_final: 0.8279 (mp0)
REVERT: F   32 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7446 (mtt-85)
REVERT: F  106 GLN cc_start: 0.8668 (mm110) cc_final: 0.8156 (mm-40)
REVERT: F  131 TYR cc_start: 0.7952 (p90) cc_final: 0.7036 (p90)
  outliers start: 91
  outliers final: 68
  residues processed: 323
  average time/residue: 0.2579
  time to fit residues: 123.6398
Evaluate side-chains
  323 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 247
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 SER
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  606 ASP
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   11 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   32 ARG
Chi-restraints excluded: chain F residue   36 GLN
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  132 THR
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  141 MET
Chi-restraints excluded: chain F residue  152 MET
Chi-restraints excluded: chain F residue  169 THR
Chi-restraints excluded: chain F residue  170 VAL
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 137 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN
F  14 ASN
F  36 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.096243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.085405 restraints weight = 35971.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.087527 restraints weight = 17156.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.088885 restraints weight = 9842.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  12838  Z= 0.232
  Angle     :  0.659  10.011  17475  Z= 0.347
  Chirality :  0.046   0.215   1940
  Planarity :  0.004   0.041   2322
  Dihedral  :  4.885  20.832   1777
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 27.77 %
    Favored  : 65.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.85 (0.20), residues: 1604
  helix:  0.96 (0.30), residues: 290
  sheet: -1.52 (0.25), residues: 422
  loop : -1.86 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F  37 
 HIS   0.005   0.001   HIS F  84 
 PHE   0.022   0.002   PHE B 110 
 TYR   0.026   0.002   TYR C  53 
 ARG   0.004   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04436 (  429)
  hydrogen bonds       : angle       5.76492 ( 1089)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       4.12786 (    4)
  covalent geometry    : bond        0.00527 (12836)
  covalent geometry    : angle       0.65595 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 256
  time to evaluate  : 1.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8484 (p)
REVERT: A  199 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8712 (t)
REVERT: A  487 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.7486 (m-10)
REVERT: A  492 GLU cc_start: 0.7774 (tp30) cc_final: 0.7101 (mt-10)
REVERT: A  670 MET cc_start: 0.7599 (mtm) cc_final: 0.7224 (mtm)
REVERT: A  750 GLU cc_start: 0.6161 (tp30) cc_final: 0.5838 (tp30)
REVERT: D   62 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: D  114 ARG cc_start: 0.9251 (tpp-160) cc_final: 0.9032 (tpp-160)
REVERT: B    6 ASN cc_start: 0.7536 (t0) cc_final: 0.7312 (t0)
REVERT: B    9 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8320 (ttm-80)
REVERT: B   67 THR cc_start: 0.8602 (m) cc_final: 0.8186 (t)
REVERT: B   92 GLU cc_start: 0.7586 (tp30) cc_final: 0.7111 (tp30)
REVERT: B   98 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8101 (mm-40)
REVERT: B  107 GLU cc_start: 0.8002 (tp30) cc_final: 0.7570 (tp30)
REVERT: B  120 GLN cc_start: 0.8214 (mt0) cc_final: 0.7486 (mt0)
REVERT: C    9 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7743 (ttp80)
REVERT: C  101 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7973 (m-80)
REVERT: C  112 ARG cc_start: 0.8956 (mmt180) cc_final: 0.8429 (mmt180)
REVERT: E   27 LYS cc_start: 0.8610 (mtmm) cc_final: 0.7962 (mtpp)
REVERT: E   79 ASP cc_start: 0.7867 (p0) cc_final: 0.7589 (p0)
REVERT: E  144 ASP cc_start: 0.8945 (p0) cc_final: 0.8565 (p0)
REVERT: E  151 MET cc_start: 0.8714 (tpt) cc_final: 0.8509 (tpp)
REVERT: E  161 MET cc_start: 0.8616 (tmm) cc_final: 0.8263 (tmm)
REVERT: F    9 ASN cc_start: 0.8175 (m-40) cc_final: 0.7894 (m110)
REVERT: F   18 ASP cc_start: 0.8787 (t0) cc_final: 0.8400 (p0)
REVERT: F   32 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7401 (mtt-85)
REVERT: F  131 TYR cc_start: 0.7929 (p90) cc_final: 0.7012 (p90)
  outliers start: 88
  outliers final: 73
  residues processed: 318
  average time/residue: 0.2760
  time to fit residues: 129.0965
Evaluate side-chains
  325 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 246
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 SER
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   11 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue   32 ARG
Chi-restraints excluded: chain F residue   36 GLN
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  104 TYR
Chi-restraints excluded: chain F residue  132 THR
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  141 MET
Chi-restraints excluded: chain F residue  169 THR
Chi-restraints excluded: chain F residue  170 VAL
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 139 optimal weight:    7.9990
   chunk 51 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    2.4784

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

Flipped N/Q/H residues before XYZ refinement:
D   6 ASN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   8 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  14 ASN
F  36 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.098641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.087878 restraints weight = 35550.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.090022 restraints weight = 16921.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.091367 restraints weight = 9616.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12838  Z= 0.138
  Angle     :  0.614   9.731  17475  Z= 0.321
  Chirality :  0.045   0.216   1940
  Planarity :  0.004   0.041   2322
  Dihedral  :  4.588  19.689   1777
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 29.25 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.65 (0.21), residues: 1604
  helix:  1.12 (0.30), residues: 289
  sheet: -1.32 (0.26), residues: 411
  loop : -1.77 (0.20), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 216 
 HIS   0.003   0.001   HIS F  84 
 PHE   0.022   0.001   PHE B 110 
 TYR   0.024   0.001   TYR C 101 
 ARG   0.006   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03901 (  429)
  hydrogen bonds       : angle       5.50940 ( 1089)
  SS BOND              : bond        0.00616 (    2)
  SS BOND              : angle       5.00426 (    4)
  covalent geometry    : bond        0.00315 (12836)
  covalent geometry    : angle       0.60961 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 264
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8647 (m-80)
REVERT: A   54 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8443 (p)
REVERT: A  199 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (t)
REVERT: A  466 TYR cc_start: 0.8009 (m-80) cc_final: 0.7714 (m-80)
REVERT: A  487 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.7312 (m-10)
REVERT: A  492 GLU cc_start: 0.7737 (tp30) cc_final: 0.6989 (mt-10)
REVERT: A  503 ASP cc_start: 0.8222 (t70) cc_final: 0.7928 (t0)
REVERT: A  509 MET cc_start: 0.8462 (tpp) cc_final: 0.7464 (mmm)
REVERT: A  670 MET cc_start: 0.7530 (mtm) cc_final: 0.7170 (mtm)
REVERT: A  750 GLU cc_start: 0.6134 (tp30) cc_final: 0.5768 (tp30)
REVERT: D   92 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8507 (mm-30)
REVERT: D  109 GLU cc_start: 0.8557 (tp30) cc_final: 0.8244 (tp30)
REVERT: B    9 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8266 (ttm-80)
REVERT: B   67 THR cc_start: 0.8503 (m) cc_final: 0.8106 (t)
REVERT: B   92 GLU cc_start: 0.7418 (tp30) cc_final: 0.6909 (tp30)
REVERT: B   98 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8088 (mm-40)
REVERT: B  107 GLU cc_start: 0.7914 (tp30) cc_final: 0.7498 (tp30)
REVERT: C    9 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7791 (ttp80)
REVERT: C   91 GLN cc_start: 0.7774 (pt0) cc_final: 0.7572 (pt0)
REVERT: C  101 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7764 (m-80)
REVERT: E   79 ASP cc_start: 0.7935 (p0) cc_final: 0.7586 (p0)
REVERT: E   92 TYR cc_start: 0.8328 (t80) cc_final: 0.7653 (m-80)
REVERT: E  144 ASP cc_start: 0.8907 (p0) cc_final: 0.8519 (p0)
REVERT: E  151 MET cc_start: 0.8666 (tpt) cc_final: 0.8460 (tpp)
REVERT: E  159 MET cc_start: 0.8480 (tpt) cc_final: 0.7402 (ttt)
REVERT: E  161 MET cc_start: 0.8558 (tmm) cc_final: 0.8149 (tmm)
REVERT: F    9 ASN cc_start: 0.8007 (m-40) cc_final: 0.7769 (m110)
REVERT: F   18 ASP cc_start: 0.8688 (t0) cc_final: 0.8349 (p0)
REVERT: F   75 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8380 (tpt-90)
REVERT: F  131 TYR cc_start: 0.7877 (p90) cc_final: 0.7006 (p90)
  outliers start: 66
  outliers final: 51
  residues processed: 309
  average time/residue: 0.3099
  time to fit residues: 141.3795
Evaluate side-chains
  313 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 256
  time to evaluate  : 1.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    6 ASN
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   11 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain F residue   14 ASN
Chi-restraints excluded: chain F residue   36 GLN
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  141 MET
Chi-restraints excluded: chain F residue  169 THR
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 120 optimal weight:    8.9990
   chunk 73 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   chunk 49 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0000
   chunk 43 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    3.4790

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

Flipped N/Q/H residues before XYZ refinement:
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  14 ASN
F  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.099123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.088258 restraints weight = 35202.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.090430 restraints weight = 16815.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.091815 restraints weight = 9624.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12838  Z= 0.163
  Angle     :  0.633  11.404  17475  Z= 0.330
  Chirality :  0.045   0.216   1940
  Planarity :  0.004   0.042   2322
  Dihedral  :  4.604  19.483   1777
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 29.99 %
    Favored  : 65.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.60 (0.21), residues: 1604
  helix:  1.03 (0.30), residues: 289
  sheet: -1.21 (0.26), residues: 410
  loop : -1.74 (0.20), residues: 905

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 216 
 HIS   0.004   0.001   HIS F  84 
 PHE   0.023   0.002   PHE B 110 
 TYR   0.024   0.002   TYR C  53 
 ARG   0.004   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  429)
  hydrogen bonds       : angle       5.51985 ( 1089)
  SS BOND              : bond        0.00765 (    2)
  SS BOND              : angle       4.66348 (    4)
  covalent geometry    : bond        0.00376 (12836)
  covalent geometry    : angle       0.62957 (17471)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 258
  time to evaluate  : 2.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8652 (m-80)
REVERT: A   54 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8492 (p)
REVERT: A  199 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8728 (t)
REVERT: A  466 TYR cc_start: 0.8109 (m-80) cc_final: 0.7781 (m-80)
REVERT: A  487 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.7337 (m-10)
REVERT: A  492 GLU cc_start: 0.7763 (tp30) cc_final: 0.7030 (mt-10)
REVERT: A  503 ASP cc_start: 0.8213 (t70) cc_final: 0.7895 (t0)
REVERT: A  509 MET cc_start: 0.8452 (tpp) cc_final: 0.7484 (mmm)
REVERT: A  670 MET cc_start: 0.7546 (mtm) cc_final: 0.7189 (mtm)
REVERT: A  750 GLU cc_start: 0.6118 (tp30) cc_final: 0.5749 (tp30)
REVERT: D   92 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8572 (mm-30)
REVERT: B    9 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8295 (ttm-80)
REVERT: B   67 THR cc_start: 0.8502 (m) cc_final: 0.8082 (t)
REVERT: B   92 GLU cc_start: 0.7448 (tp30) cc_final: 0.6962 (tp30)
REVERT: B  107 GLU cc_start: 0.7931 (tp30) cc_final: 0.7533 (tp30)
REVERT: C    9 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7665 (ttp80)
REVERT: C   11 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.6969 (mp10)
REVERT: C   91 GLN cc_start: 0.7743 (pt0) cc_final: 0.7535 (pt0)
REVERT: C  101 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7752 (m-80)
REVERT: C  112 ARG cc_start: 0.8977 (mmt180) cc_final: 0.8486 (mmt180)
REVERT: E    4 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8792 (mmtm)
REVERT: E   79 ASP cc_start: 0.7942 (p0) cc_final: 0.7593 (p0)
REVERT: E   92 TYR cc_start: 0.8427 (t80) cc_final: 0.7693 (m-80)
REVERT: E  144 ASP cc_start: 0.8908 (p0) cc_final: 0.8512 (p0)
REVERT: E  159 MET cc_start: 0.8471 (tpt) cc_final: 0.7288 (ttp)
REVERT: E  161 MET cc_start: 0.8488 (tmm) cc_final: 0.8066 (tmm)
REVERT: F    4 LYS cc_start: 0.5971 (tmtt) cc_final: 0.5431 (tptp)
REVERT: F   18 ASP cc_start: 0.8758 (t0) cc_final: 0.8382 (p0)
REVERT: F  131 TYR cc_start: 0.7887 (p90) cc_final: 0.7002 (p90)
  outliers start: 61
  outliers final: 52
  residues processed: 299
  average time/residue: 0.3603
  time to fit residues: 163.2916
Evaluate side-chains
  312 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 253
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 TRP
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    8 ASN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   11 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain F residue   14 ASN
Chi-restraints excluded: chain F residue   36 GLN
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  141 MET
Chi-restraints excluded: chain F residue  169 THR
Chi-restraints excluded: chain F residue  174 GLN
Chi-restraints excluded: chain F residue  199 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 129 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 134 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 119 optimal weight:   10.0000
   chunk 127 optimal weight:    4.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
D   6 ASN
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN
F  14 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.097618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.086871 restraints weight = 35780.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.088995 restraints weight = 17031.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.090320 restraints weight = 9712.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12838  Z= 0.184
  Angle     :  0.648  11.468  17475  Z= 0.338
  Chirality :  0.046   0.215   1940
  Planarity :  0.004   0.042   2322
  Dihedral  :  4.656  19.451   1777
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 29.84 %
    Favored  : 65.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.62 (0.21), residues: 1604
  helix:  1.00 (0.30), residues: 289
  sheet: -1.26 (0.26), residues: 411
  loop : -1.73 (0.20), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 216 
 HIS   0.005   0.001   HIS F  84 
 PHE   0.024   0.002   PHE B 110 
 TYR   0.022   0.002   TYR C 101 
 ARG   0.005   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (  429)
  hydrogen bonds       : angle       5.57979 ( 1089)
  SS BOND              : bond        0.00739 (    2)
  SS BOND              : angle       4.67121 (    4)
  covalent geometry    : bond        0.00420 (12836)
  covalent geometry    : angle       0.64448 (17471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4647.60 seconds
wall clock time: 88 minutes 8.99 seconds (5288.99 seconds total)