Starting phenix.real_space_refine
on Wed Aug  5 14:37:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sx6_55332/08_2026/9sx6_55332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sx6_55332/08_2026/9sx6_55332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sx6_55332/08_2026/9sx6_55332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sx6_55332/08_2026/9sx6_55332.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sx6_55332/08_2026/9sx6_55332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sx6_55332/08_2026/9sx6_55332.map"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      58      5.49       5
     S      24      5.16       5
     C    6264      2.51       5
     N    1735      2.21       5
     O    2052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10133
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "H"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "E"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "G"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "F"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1118
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "Y"
      Number of atoms: 607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 607
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "Z"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 582
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
  Time building chain proxies: 2.02, per 1000 atoms: 0.20
  Number of scatterers: 10133
  At special positions: 0
  Unit cell: (56.763, 127.041, 138.754, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      58     15.00
     O    2052      8.00
     N    1735      7.00
     C    6264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 343.1 milliseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 16 sheets defined
      44.2% alpha, 22.3% beta
      28 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 24
      removed outlier: 4.029A  pdb=" N   SER A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 4.044A  pdb=" N   GLU A  49 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 75
      removed outlier: 4.249A  pdb=" N   ASN A  75 " --> pdb=" O   LEU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 98
    Processing helix  chain 'A' and resid 117 through 126
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.696A  pdb=" N   MET A 137 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 19 through 24
      removed outlier: 3.925A  pdb=" N   SER H  24 " --> pdb=" O   ALA H  20 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 44 through 56
      removed outlier: 3.747A  pdb=" N   GLU H  49 " --> pdb=" O   PRO H  45 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER H  50 " --> pdb=" O   ALA H  46 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 75
      removed outlier: 4.244A  pdb=" N   ASN H  75 " --> pdb=" O   LEU H  71 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 98
    Processing helix  chain 'H' and resid 117 through 126
    Processing helix  chain 'H' and resid 129 through 137
      removed outlier: 3.657A  pdb=" N   MET H 137 " --> pdb=" O   VAL H 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 24
      removed outlier: 4.014A  pdb=" N   SER C  24 " --> pdb=" O   ALA C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 57
    Processing helix  chain 'C' and resid 62 through 75
      removed outlier: 4.528A  pdb=" N   ASN C  75 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 95
      removed outlier: 3.993A  pdb=" N   SER C  95 " --> pdb=" O   ASN C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 127
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'B' and resid 19 through 24
    Processing helix  chain 'B' and resid 44 through 57
      removed outlier: 3.708A  pdb=" N   GLU B  49 " --> pdb=" O   PRO B  45 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN B  57 " --> pdb=" O   GLN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 75
      removed outlier: 4.025A  pdb=" N   ASN B  75 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 96
    Processing helix  chain 'B' and resid 117 through 126
    Processing helix  chain 'B' and resid 129 through 136
    Processing helix  chain 'E' and resid 19 through 25
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.829A  pdb=" N   GLU E  49 " --> pdb=" O   PRO E  45 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   SER E  50 " --> pdb=" O   ALA E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 75
      removed outlier: 4.151A  pdb=" N   ASN E  75 " --> pdb=" O   LEU E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 98
    Processing helix  chain 'E' and resid 117 through 127
    Processing helix  chain 'E' and resid 129 through 137
      removed outlier: 3.749A  pdb=" N   MET E 137 " --> pdb=" O   VAL E 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 24
      removed outlier: 3.737A  pdb=" N   SER D  24 " --> pdb=" O   ALA D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 57
      removed outlier: 3.822A  pdb=" N   ASN D  57 " --> pdb=" O   GLN D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 75
      removed outlier: 4.104A  pdb=" N   ASN D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 98
      removed outlier: 3.757A  pdb=" N   ASP D  96 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 126
    Processing helix  chain 'D' and resid 129 through 136
      removed outlier: 3.535A  pdb=" N   ARG D 136 " --> pdb=" O   THR D 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 24
      removed outlier: 4.167A  pdb=" N   SER G  24 " --> pdb=" O   ALA G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 44 through 57
      removed outlier: 3.710A  pdb=" N   ASN G  57 " --> pdb=" O   GLN G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 74
    Processing helix  chain 'G' and resid 90 through 98
      removed outlier: 3.813A  pdb=" N   SER G  95 " --> pdb=" O   ASN G  91 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP G  96 " --> pdb=" O   ASN G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 117 through 126
    Processing helix  chain 'G' and resid 129 through 136
      removed outlier: 3.587A  pdb=" N   ARG G 136 " --> pdb=" O   THR G 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 19 through 24
    Processing helix  chain 'F' and resid 44 through 56
    Processing helix  chain 'F' and resid 62 through 75
      removed outlier: 4.054A  pdb=" N   ASN F  75 " --> pdb=" O   LEU F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 98
      removed outlier: 3.562A  pdb=" N   SER F  95 " --> pdb=" O   ASN F  91 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP F  96 " --> pdb=" O   ASN F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 117 through 126
    Processing helix  chain 'F' and resid 129 through 136
      removed outlier: 3.589A  pdb=" N   ARG F 136 " --> pdb=" O   THR F 132 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9
      removed outlier: 3.779A  pdb=" N   CYS A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
    Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 9
    Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 17
    Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 8
      removed outlier: 3.790A  pdb=" N   HIS C 111 " --> pdb=" O   GLN C 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 15 through 17
    Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 9
      removed outlier: 3.600A  pdb=" N   HIS B 111 " --> pdb=" O   GLN B 108 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 17
    Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 8
      removed outlier: 3.973A  pdb=" N   CYS E  39 " --> pdb=" O   GLY E  35 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 15 through 17
    Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 9
      removed outlier: 3.803A  pdb=" N   CYS D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 15 through 17
    Processing sheet with id=AB4, first strand: chain 'G' and resid 3 through 9
      removed outlier: 3.851A  pdb=" N   GLY G   4 " --> pdb=" O   GLY G 107 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   CYS G  39 " --> pdb=" O   GLY G  35 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 15 through 17
    Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 8
      removed outlier: 3.956A  pdb=" N   GLY F   4 " --> pdb=" O   GLY F 107 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   CYS F  39 " --> pdb=" O   GLY F  35 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 16 through 17

    449 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      68 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 1.67

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2610
        1.33 -     1.45: 2070
        1.45 -     1.57: 5594
        1.57 -     1.69: 114
        1.69 -     1.80: 40
  Bond restraints: 10428
  Sorted by residual:
  bond pdb=" O3'  DT Z  -6 "
       pdb=" P    DT Z  -5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.687 -0.080 1.20e-02 6.94e+03 4.40e+01
  bond pdb=" C3'  DT Z  12 "
       pdb=" C2'  DT Z  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.18e+01
  bond pdb=" C3'  DC Z  20 "
       pdb=" C2'  DC Z  20 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" C3'  DC Z  10 "
       pdb=" C2'  DC Z  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" C3'  DA Z  -1 "
       pdb=" C2'  DA Z  -1 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 6.67e+00
  ... (remaining 10423 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 14256
        3.45 -     6.91: 78
        6.91 -    10.36: 3
       10.36 -    13.82: 0
       13.82 -    17.27: 2
  Bond angle restraints: 14339
  Sorted by residual:
  angle pdb=" C3'  DT Z  -6 "
        pdb=" O3'  DT Z  -6 "
        pdb=" P    DT Z  -5 "
      ideal   model   delta    sigma   weight residual
     119.70  112.41    7.29 1.20e+00 6.94e-01 3.69e+01
  angle pdb=" O3'  DT Z  -6 "
        pdb=" P    DT Z  -5 "
        pdb=" OP2  DT Z  -5 "
      ideal   model   delta    sigma   weight residual
     108.00  125.27  -17.27 3.00e+00 1.11e-01 3.31e+01
  angle pdb=" O3'  DT Z  -6 "
        pdb=" P    DT Z  -5 "
        pdb=" OP1  DT Z  -5 "
      ideal   model   delta    sigma   weight residual
     108.00   93.47   14.53 3.00e+00 1.11e-01 2.34e+01
  angle pdb=" N3   DT Z  12 "
        pdb=" C4   DT Z  12 "
        pdb=" O4   DT Z  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.56   -2.66 6.00e-01 2.78e+00 1.97e+01
  angle pdb=" O4'  DA Y   6 "
        pdb=" C4'  DA Y   6 "
        pdb=" C3'  DA Y   6 "
      ideal   model   delta    sigma   weight residual
     106.00  103.38    2.62 6.00e-01 2.78e+00 1.91e+01
  ... (remaining 14334 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.75: 5646
       31.75 -    63.49: 541
       63.49 -    95.24: 20
       95.24 -   126.99: 0
      126.99 -   158.74: 3
  Dihedral angle restraints: 6210
    sinusoidal: 2954
      harmonic: 3256
  Sorted by residual:
  dihedral pdb=" CA  LYS H  13 "
           pdb=" C   LYS H  13 "
           pdb=" N   ASN H  14 "
           pdb=" CA  ASN H  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.69  -22.31     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  LYS F 101 "
           pdb=" C   LYS F 101 "
           pdb=" N   GLU F 102 "
           pdb=" CA  GLU F 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.60   21.40     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LYS F  13 "
           pdb=" C   LYS F  13 "
           pdb=" N   ASN F  14 "
           pdb=" CA  ASN F  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.29  -20.71     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 6207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1580
       0.116 -    0.232: 51
       0.232 -    0.347: 0
       0.347 -    0.463: 0
       0.463 -    0.579: 1
  Chirality restraints: 1632
  Sorted by residual:
  chirality pdb=" P    DA Y   6 "
            pdb=" OP1  DA Y   6 "
            pdb=" OP2  DA Y   6 "
            pdb=" O5'  DA Y   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.91   -0.58 2.00e-01 2.50e+01 8.39e+00
  chirality pdb=" CA  ASP D  82 "
            pdb=" N   ASP D  82 "
            pdb=" C   ASP D  82 "
            pdb=" CB  ASP D  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" C3'  DA Y -13 "
            pdb=" C4'  DA Y -13 "
            pdb=" O3'  DA Y -13 "
            pdb=" C2'  DA Y -13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.54   -0.19 2.00e-01 2.50e+01 8.65e-01
  ... (remaining 1629 not shown)

  Planarity restraints: 1658
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  91 "   -0.009 2.00e-02 2.50e+03   1.72e-02 2.96e+00
        pdb=" CG  ASN B  91 "    0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  91 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  91 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D  82 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.64e+00
        pdb=" CG  ASP D  82 "   -0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASP D  82 "    0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP D  82 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  52 "    0.011 2.00e-02 2.50e+03   1.19e-02 2.48e+00
        pdb=" CG  PHE A  52 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  52 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  52 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  52 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  52 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  52 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1655 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.96: 4727
        2.96 -     3.45: 10213
        3.45 -     3.93: 17035
        3.93 -     4.42: 19227
        4.42 -     4.90: 30548
  Nonbonded interactions: 81750
  Sorted by model distance:
  nonbonded pdb=" O5'  DA Z  17 "
            pdb=" O4'  DA Z  17 "
     model   vdw
     2.478 2.432
  nonbonded pdb=" O5'  DG Y   2 "
            pdb=" O4'  DG Y   2 "
     model   vdw
     2.483 2.432
  nonbonded pdb=" O   SER B 126 "
            pdb=" OG  SER B 126 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" O5'  DG Y   3 "
            pdb=" O4'  DG Y   3 "
     model   vdw
     2.512 2.432
  nonbonded pdb=" O5'  DC Z  -2 "
            pdb=" O4'  DC Z  -2 "
     model   vdw
     2.513 2.432
  ... (remaining 81745 not shown)

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

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:             2.750
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.740
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  10428  Z= 0.305
  Angle     :  0.752  17.271  14339  Z= 0.496
  Chirality :  0.049   0.579   1632
  Planarity :  0.004   0.043   1658
  Dihedral  : 20.982 158.737   4066
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.59 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 27.08 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1080
  helix:  0.20 (0.24), residues: 456
  sheet:  0.63 (0.27), residues: 384
  loop : -2.47 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  15 
 TYR   0.009   0.001   TYR B 120 
 PHE   0.027   0.001   PHE A  52 
 TRP   0.014   0.002   TRP D 115 
 HIS   0.004   0.002   HIS F 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00455 /  0.31 (10428)
  covalent geometry    : angle       0.75195 /  0.50 (14339)
  hydrogen bonds       : bond        0.12576 /  8.80 (  517)
  hydrogen bonds       : angle       5.87953 /  4.11 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 244
  time to evaluate  : 0.255 
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   30 ILE cc_start: 0.8623 (pp) cc_final: 0.8304 (pt)
REVERT: A   32 ILE cc_start: 0.8621 (tp) cc_final: 0.8337 (tt)
REVERT: A   87 ILE cc_start: 0.7930 (mt) cc_final: 0.7690 (mt)
REVERT: F   51 TYR cc_start: 0.7701 (t80) cc_final: 0.7479 (t80)
  outliers start: 42
  outliers final: 10
  residues processed: 272
  average time/residue: 0.0955
  time to fit residues: 36.3194
Evaluate side-chains
  171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain C residue   43 ARG
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue  109 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0000
   chunk 106 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
A  56 ASN
A  85 ASN
C  33 ASN
C  38 ASN
C  85 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
B  77 ASN
B  91 ASN
E  85 ASN
** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN
D  75 ASN
G  85 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.056067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.042835 restraints weight = 44738.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.044210 restraints weight = 21408.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.045125 restraints weight = 13331.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.045734 restraints weight = 9728.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.046046 restraints weight = 7807.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10428  Z= 0.219
  Angle     :  0.693   7.373  14339  Z= 0.391
  Chirality :  0.048   0.313   1632
  Planarity :  0.004   0.037   1658
  Dihedral  : 21.454 162.698   1839
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  7.41 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 23.41 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.26), residues: 1080
  helix:  0.10 (0.24), residues: 464
  sheet:  0.92 (0.31), residues: 304
  loop : -1.53 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  23 
 TYR   0.013   0.001   TYR B 120 
 PHE   0.022   0.002   PHE D  52 
 TRP   0.013   0.002   TRP A 115 
 HIS   0.003   0.001   HIS F 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00476 /  0.22 (10428)
  covalent geometry    : angle       0.69313 /  0.39 (14339)
  hydrogen bonds       : bond        0.05083 /  3.38 (  517)
  hydrogen bonds       : angle       5.38246 /  3.80 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 170
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8318 (t0)
REVERT: A   51 TYR cc_start: 0.9181 (t80) cc_final: 0.8970 (t80)
REVERT: A  118 VAL cc_start: 0.9410 (t) cc_final: 0.8991 (p)
REVERT: C   33 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8140 (p0)
REVERT: C   49 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: C   53 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8334 (mm110)
REVERT: B   49 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: B   95 SER cc_start: 0.8971 (t) cc_final: 0.8702 (p)
REVERT: B  122 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8593 (tp-100)
REVERT: E   88 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7911 (pp)
REVERT: D   98 LYS cc_start: 0.9201 (mtpp) cc_final: 0.8855 (mtmm)
REVERT: G   49 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: F   49 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8304 (tm-30)
REVERT: F   80 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7603 (mm-30)
  outliers start: 54
  outliers final: 23
  residues processed: 209
  average time/residue: 0.0909
  time to fit residues: 27.1985
Evaluate side-chains
  180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   33 ASN
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   28 SER
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   89 ILE
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   55 PHE
Chi-restraints excluded: chain F residue  109 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
A 119 GLN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  14 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.054693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.041375 restraints weight = 44136.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.042631 restraints weight = 22127.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.043491 restraints weight = 14248.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.044059 restraints weight = 10590.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.044425 restraints weight = 8629.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10428  Z= 0.251
  Angle     :  0.671   6.978  14339  Z= 0.374
  Chirality :  0.047   0.311   1632
  Planarity :  0.004   0.039   1658
  Dihedral  : 21.476 163.717   1828
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  8.06 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 23.31 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.26), residues: 1080
  helix:  0.16 (0.24), residues: 464
  sheet:  1.06 (0.32), residues: 272
  loop : -1.69 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  34 
 TYR   0.022   0.001   TYR F  51 
 PHE   0.022   0.002   PHE A  52 
 TRP   0.012   0.002   TRP A 115 
 HIS   0.004   0.002   HIS A 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.25 (10428)
  covalent geometry    : angle       0.67086 /  0.37 (14339)
  hydrogen bonds       : bond        0.04820 /  3.14 (  517)
  hydrogen bonds       : angle       5.23208 /  3.70 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 163
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8643 (mmmt)
REVERT: C   33 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (p0)
REVERT: C   49 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8452 (tm-30)
REVERT: C  113 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6878 (mt-10)
REVERT: B   49 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: B   95 SER cc_start: 0.8906 (t) cc_final: 0.8635 (p)
REVERT: B  122 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8445 (tp-100)
REVERT: E   88 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7928 (pp)
REVERT: D   49 GLU cc_start: 0.8692 (tp30) cc_final: 0.8185 (tp30)
REVERT: D   53 GLN cc_start: 0.9414 (mm-40) cc_final: 0.9019 (mm-40)
REVERT: G   49 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: G  108 GLN cc_start: 0.7691 (mp10) cc_final: 0.7474 (mp10)
REVERT: F   49 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: F   80 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7511 (mm-30)
REVERT: F  117 LYS cc_start: 0.9093 (tttp) cc_final: 0.8843 (ttmm)
  outliers start: 48
  outliers final: 31
  residues processed: 198
  average time/residue: 0.0934
  time to fit residues: 26.4711
Evaluate side-chains
  177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain H residue  106 ILE
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   33 ASN
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain G residue   24 SER
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain G residue   89 ILE
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   99 LEU
Chi-restraints excluded: chain F residue  109 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 70 optimal weight:    0.3980
   chunk 100 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  33 ASN
C  38 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 122 GLN
E 108 GLN
G  38 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.056302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.043025 restraints weight = 43272.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044343 restraints weight = 20808.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.045250 restraints weight = 13025.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.045831 restraints weight = 9473.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.046258 restraints weight = 7645.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10428  Z= 0.149
  Angle     :  0.629   7.398  14339  Z= 0.353
  Chirality :  0.046   0.319   1632
  Planarity :  0.004   0.065   1658
  Dihedral  : 21.443 164.179   1828
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  7.59 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.81 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.26), residues: 1080
  helix:  0.17 (0.24), residues: 464
  sheet:  1.03 (0.32), residues: 272
  loop : -1.69 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  23 
 TYR   0.020   0.001   TYR F  51 
 PHE   0.022   0.001   PHE C  58 
 TRP   0.012   0.002   TRP D 115 
 HIS   0.005   0.002   HIS B 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 (10428)
  covalent geometry    : angle       0.62876 /  0.35 (14339)
  hydrogen bonds       : bond        0.03946 /  2.59 (  517)
  hydrogen bonds       : angle       5.03461 /  3.56 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 171
  time to evaluate  : 0.402 
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    7 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (t0)
REVERT: A  101 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8717 (mmmt)
REVERT: A  119 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8251 (mt0)
REVERT: C   33 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8266 (p0)
REVERT: C   41 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7734 (mt-10)
REVERT: C   49 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: C   69 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8896 (mtmm)
REVERT: C  113 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6990 (mt-10)
REVERT: B   49 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: B   62 GLN cc_start: 0.7892 (mp10) cc_final: 0.7675 (mp10)
REVERT: B   95 SER cc_start: 0.8898 (t) cc_final: 0.8630 (p)
REVERT: B  122 GLN cc_start: 0.8800 (tp40) cc_final: 0.8347 (tp-100)
REVERT: E   88 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7882 (pp)
REVERT: D   49 GLU cc_start: 0.8626 (tp30) cc_final: 0.8020 (tp30)
REVERT: D   53 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8900 (mm-40)
REVERT: G   49 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: G  108 GLN cc_start: 0.7836 (mp10) cc_final: 0.7555 (mp10)
REVERT: G  113 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7076 (mt-10)
REVERT: G  117 LYS cc_start: 0.9422 (tptm) cc_final: 0.9154 (mmmm)
REVERT: F   49 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8315 (tm-30)
REVERT: F   55 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8566 (t80)
REVERT: F   80 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7475 (mm-30)
  outliers start: 43
  outliers final: 26
  residues processed: 203
  average time/residue: 0.0862
  time to fit residues: 25.1453
Evaluate side-chains
  179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   11 ASP
Chi-restraints excluded: chain C residue   33 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue   55 PHE
Chi-restraints excluded: chain F residue   99 LEU
Chi-restraints excluded: chain F residue  109 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.055224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.042036 restraints weight = 44450.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.043316 restraints weight = 22173.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.044204 restraints weight = 14234.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.044730 restraints weight = 10499.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.045144 restraints weight = 8608.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10428  Z= 0.186
  Angle     :  0.632   9.147  14339  Z= 0.351
  Chirality :  0.046   0.314   1632
  Planarity :  0.004   0.041   1658
  Dihedral  : 21.430 165.245   1827
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.22 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.70 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1080
  helix:  0.16 (0.24), residues: 464
  sheet:  1.04 (0.32), residues: 272
  loop : -1.60 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  23 
 TYR   0.021   0.001   TYR F  51 
 PHE   0.022   0.001   PHE C  58 
 TRP   0.010   0.002   TRP D 115 
 HIS   0.004   0.002   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.19 (10428)
  covalent geometry    : angle       0.63217 /  0.35 (14339)
  hydrogen bonds       : bond        0.04092 /  2.71 (  517)
  hydrogen bonds       : angle       4.98740 /  3.53 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 155
  time to evaluate  : 0.407 
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    7 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8656 (t0)
REVERT: A  122 GLN cc_start: 0.8668 (pp30) cc_final: 0.8364 (pp30)
REVERT: C   49 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8478 (tm-30)
REVERT: C   69 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8857 (mtmm)
REVERT: C  113 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7078 (mt-10)
REVERT: B   49 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7972 (tm-30)
REVERT: B  122 GLN cc_start: 0.8932 (tp40) cc_final: 0.8411 (tp-100)
REVERT: E   88 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7872 (pp)
REVERT: D   49 GLU cc_start: 0.8669 (tp30) cc_final: 0.8011 (tp30)
REVERT: D   53 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8982 (mm-40)
REVERT: G   49 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: G   54 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9077 (p)
REVERT: G  108 GLN cc_start: 0.7939 (mp10) cc_final: 0.7477 (mp10)
REVERT: G  113 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7025 (mt-10)
REVERT: G  117 LYS cc_start: 0.9459 (tptm) cc_final: 0.9171 (mmmm)
REVERT: F   49 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8361 (tm-30)
REVERT: F   80 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7421 (mm-30)
  outliers start: 39
  outliers final: 29
  residues processed: 183
  average time/residue: 0.0833
  time to fit residues: 21.7270
Evaluate side-chains
  178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   55 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   28 SER
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue   55 PHE
Chi-restraints excluded: chain F residue  109 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.054844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.041450 restraints weight = 45017.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.042726 restraints weight = 22968.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.043586 restraints weight = 14970.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.044186 restraints weight = 11230.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.044589 restraints weight = 9163.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10428  Z= 0.167
  Angle     :  0.614   7.487  14339  Z= 0.344
  Chirality :  0.046   0.314   1632
  Planarity :  0.004   0.040   1658
  Dihedral  : 21.416 166.023   1827
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.31 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 25.50 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.26), residues: 1080
  helix:  0.19 (0.24), residues: 464
  sheet:  1.01 (0.32), residues: 272
  loop : -1.54 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.020   0.001   TYR F  51 
 PHE   0.025   0.001   PHE C  48 
 TRP   0.011   0.002   TRP A 115 
 HIS   0.004   0.002   HIS G 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.17 (10428)
  covalent geometry    : angle       0.61395 /  0.34 (14339)
  hydrogen bonds       : bond        0.03848 /  2.52 (  517)
  hydrogen bonds       : angle       4.89097 /  3.46 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 159
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 GLN cc_start: 0.8583 (pp30) cc_final: 0.8362 (pp30)
REVERT: C   49 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8466 (tm-30)
REVERT: C   69 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8865 (mtmm)
REVERT: C  113 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7120 (mt-10)
REVERT: B   49 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: B  122 GLN cc_start: 0.8908 (tp40) cc_final: 0.8377 (tp-100)
REVERT: E   88 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7859 (pp)
REVERT: D   49 GLU cc_start: 0.8650 (tp30) cc_final: 0.7965 (tp30)
REVERT: D   53 GLN cc_start: 0.9366 (mm-40) cc_final: 0.8919 (mm-40)
REVERT: D  100 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7885 (p0)
REVERT: D  101 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8622 (mmmm)
REVERT: G   49 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: G  108 GLN cc_start: 0.8073 (mp10) cc_final: 0.7484 (mp10)
REVERT: G  113 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6966 (mt-10)
REVERT: F   49 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8374 (tm-30)
REVERT: F   80 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7578 (mm-30)
  outliers start: 42
  outliers final: 26
  residues processed: 191
  average time/residue: 0.0848
  time to fit residues: 23.4401
Evaluate side-chains
  173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   55 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue   55 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
A 119 GLN
** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 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 = 0.3311 r_free = 0.3311 target = 0.055202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.041612 restraints weight = 44193.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.042875 restraints weight = 22519.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.043760 restraints weight = 14677.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.044270 restraints weight = 10940.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.044690 restraints weight = 9095.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10428  Z= 0.177
  Angle     :  0.630  10.499  14339  Z= 0.348
  Chirality :  0.046   0.312   1632
  Planarity :  0.004   0.041   1658
  Dihedral  : 21.394 166.899   1825
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.41 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.29 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.26), residues: 1080
  helix:  0.20 (0.24), residues: 464
  sheet:  1.37 (0.32), residues: 256
  loop : -1.60 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.017   0.001   TYR F  51 
 PHE   0.023   0.001   PHE A  52 
 TRP   0.012   0.002   TRP D 115 
 HIS   0.004   0.002   HIS G 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.18 (10428)
  covalent geometry    : angle       0.63037 /  0.35 (14339)
  hydrogen bonds       : bond        0.03912 /  2.57 (  517)
  hydrogen bonds       : angle       4.89688 /  3.46 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 160
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8812 (tp30) cc_final: 0.8551 (tp30)
REVERT: C   49 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: C   53 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8394 (mm110)
REVERT: C   69 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8833 (mtmm)
REVERT: C  113 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: B   49 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: B   95 SER cc_start: 0.8909 (t) cc_final: 0.8660 (p)
REVERT: B  122 GLN cc_start: 0.8902 (tp40) cc_final: 0.8360 (tp-100)
REVERT: E   88 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7824 (pp)
REVERT: D   49 GLU cc_start: 0.8665 (tp30) cc_final: 0.7960 (tp30)
REVERT: D   53 GLN cc_start: 0.9379 (mm-40) cc_final: 0.8927 (mm-40)
REVERT: D  100 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7895 (p0)
REVERT: D  101 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8823 (mmmm)
REVERT: G   49 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7936 (tm-30)
REVERT: F   49 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: F   80 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7587 (mm-30)
  outliers start: 37
  outliers final: 28
  residues processed: 187
  average time/residue: 0.0914
  time to fit residues: 24.5518
Evaluate side-chains
  174 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   55 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0050
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.055738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.042224 restraints weight = 43362.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.043528 restraints weight = 21135.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.044435 restraints weight = 13442.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.045032 restraints weight = 9848.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.045444 restraints weight = 8005.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10428  Z= 0.140
  Angle     :  0.623   7.320  14339  Z= 0.345
  Chirality :  0.046   0.315   1632
  Planarity :  0.004   0.040   1658
  Dihedral  : 21.389 167.359   1825
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  6.94 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 25.89 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.26), residues: 1080
  helix:  0.18 (0.24), residues: 456
  sheet:  1.35 (0.32), residues: 256
  loop : -1.60 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.016   0.001   TYR F  51 
 PHE   0.029   0.001   PHE A  52 
 TRP   0.010   0.002   TRP A 115 
 HIS   0.004   0.002   HIS A 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 (10428)
  covalent geometry    : angle       0.62256 /  0.34 (14339)
  hydrogen bonds       : bond        0.03598 /  2.37 (  517)
  hydrogen bonds       : angle       4.81185 /  3.40 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8707 (tp30) cc_final: 0.8436 (tp30)
REVERT: C   49 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8462 (tm-30)
REVERT: C   69 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8842 (mtmm)
REVERT: C  113 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7098 (mt-10)
REVERT: B   26 PHE cc_start: 0.8464 (m-80) cc_final: 0.8209 (m-80)
REVERT: B   49 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8073 (tm-30)
REVERT: B   95 SER cc_start: 0.8864 (t) cc_final: 0.8616 (p)
REVERT: B  122 GLN cc_start: 0.8897 (tp40) cc_final: 0.8358 (tp-100)
REVERT: E   88 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7865 (pp)
REVERT: E  121 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8874 (tm-30)
REVERT: D   49 GLU cc_start: 0.8687 (tp30) cc_final: 0.7992 (tp30)
REVERT: D   53 GLN cc_start: 0.9372 (mm-40) cc_final: 0.8948 (mm-40)
REVERT: D  100 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7783 (p0)
REVERT: D  101 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8608 (mmmm)
REVERT: G   49 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7876 (tm-30)
REVERT: G  117 LYS cc_start: 0.9489 (tptm) cc_final: 0.9163 (mmmm)
REVERT: F   49 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: F   55 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8672 (t80)
REVERT: F   80 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7580 (mm-30)
REVERT: F  122 GLN cc_start: 0.8814 (mp10) cc_final: 0.8499 (mp10)
  outliers start: 38
  outliers final: 30
  residues processed: 185
  average time/residue: 0.0957
  time to fit residues: 25.2410
Evaluate side-chains
  177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   55 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   28 SER
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain G residue   89 ILE
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   55 PHE
Chi-restraints excluded: chain F residue  103 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 106 optimal weight:   30.0000
   chunk 76 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 94 optimal weight:    0.3980
   chunk 66 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 119 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.054970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.041553 restraints weight = 44298.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.042797 restraints weight = 22640.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.043643 restraints weight = 14802.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.044247 restraints weight = 11127.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.044617 restraints weight = 9118.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10428  Z= 0.166
  Angle     :  0.634   7.162  14339  Z= 0.352
  Chirality :  0.046   0.311   1632
  Planarity :  0.004   0.040   1658
  Dihedral  : 21.397 168.485   1825
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.31 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 25.99 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.26), residues: 1080
  helix:  0.25 (0.24), residues: 456
  sheet:  1.33 (0.33), residues: 256
  loop : -1.61 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  70 
 TYR   0.015   0.001   TYR F  51 
 PHE   0.043   0.002   PHE B  52 
 TRP   0.014   0.002   TRP A 115 
 HIS   0.004   0.002   HIS G 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 (10428)
  covalent geometry    : angle       0.63433 /  0.35 (14339)
  hydrogen bonds       : bond        0.03756 /  2.44 (  517)
  hydrogen bonds       : angle       4.80352 /  3.40 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.361 
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  121 GLU cc_start: 0.8789 (tp30) cc_final: 0.8508 (tp30)
REVERT: C   27 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8469 (p0)
REVERT: C   49 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: C   69 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8830 (mtmm)
REVERT: C  113 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7186 (mt-10)
REVERT: B   26 PHE cc_start: 0.8489 (m-80) cc_final: 0.8277 (m-80)
REVERT: B   49 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: B   95 SER cc_start: 0.8849 (t) cc_final: 0.8581 (p)
REVERT: B  122 GLN cc_start: 0.8890 (tp40) cc_final: 0.8350 (tp-100)
REVERT: E   88 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7836 (pp)
REVERT: D   49 GLU cc_start: 0.8651 (tp30) cc_final: 0.7930 (tp30)
REVERT: D   53 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8950 (mm-40)
REVERT: D  100 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7870 (p0)
REVERT: D  101 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8851 (mmmm)
REVERT: G   49 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7905 (tm-30)
REVERT: G  117 LYS cc_start: 0.9472 (tptm) cc_final: 0.9256 (mmmm)
REVERT: F   49 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: F   55 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8745 (t80)
REVERT: F   80 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7575 (mm-30)
  outliers start: 40
  outliers final: 31
  residues processed: 180
  average time/residue: 0.0837
  time to fit residues: 21.7473
Evaluate side-chains
  179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue   27 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   55 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   28 SER
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   55 PHE
Chi-restraints excluded: chain F residue  103 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 57 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 27 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    1.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.055555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.042167 restraints weight = 43916.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.043456 restraints weight = 21693.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.044351 restraints weight = 13927.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.044905 restraints weight = 10299.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.045353 restraints weight = 8429.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10428  Z= 0.191
  Angle     :  0.649   7.082  14339  Z= 0.359
  Chirality :  0.046   0.309   1632
  Planarity :  0.004   0.043   1658
  Dihedral  : 21.408 169.311   1825
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.13 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 26.69 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.26), residues: 1080
  helix:  0.21 (0.24), residues: 456
  sheet:  1.28 (0.32), residues: 256
  loop : -1.60 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.015   0.001   TYR F  51 
 PHE   0.030   0.002   PHE B  52 
 TRP   0.012   0.002   TRP A 115 
 HIS   0.004   0.002   HIS G 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00426 /  0.19 (10428)
  covalent geometry    : angle       0.64892 /  0.36 (14339)
  hydrogen bonds       : bond        0.03842 /  2.49 (  517)
  hydrogen bonds       : angle       4.84149 /  3.42 ( 1423)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 0.391 
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  121 GLU cc_start: 0.8785 (tp30) cc_final: 0.8533 (tp30)
REVERT: C   27 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8493 (p0)
REVERT: C   49 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: C   69 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8817 (mtmm)
REVERT: C  113 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7261 (mt-10)
REVERT: B   49 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: B   95 SER cc_start: 0.8853 (t) cc_final: 0.8581 (p)
REVERT: B  122 GLN cc_start: 0.8926 (tp40) cc_final: 0.8431 (tp-100)
REVERT: E   34 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7760 (tmt90)
REVERT: E   88 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7825 (pp)
REVERT: E  121 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8939 (tm-30)
REVERT: D   49 GLU cc_start: 0.8682 (tp30) cc_final: 0.7950 (tp30)
REVERT: D   53 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8974 (mm-40)
REVERT: D  100 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7753 (p0)
REVERT: D  101 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8903 (mmmt)
REVERT: G   49 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: G  117 LYS cc_start: 0.9471 (tptm) cc_final: 0.9250 (mmmm)
REVERT: F   49 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8461 (tm-30)
REVERT: F   55 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8751 (t80)
REVERT: F   80 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7524 (mm-30)
  outliers start: 40
  outliers final: 30
  residues processed: 179
  average time/residue: 0.0974
  time to fit residues: 24.8131
Evaluate side-chains
  178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   55 PHE
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain C residue   27 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   55 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   55 PHE
Chi-restraints excluded: chain F residue  103 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   7 ASN
** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN
** G 108 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 = 0.3321 r_free = 0.3321 target = 0.055293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.041764 restraints weight = 43669.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.043019 restraints weight = 21629.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.043884 restraints weight = 13919.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.044482 restraints weight = 10352.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.044888 restraints weight = 8424.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10428  Z= 0.186
  Angle     :  0.648   6.984  14339  Z= 0.358
  Chirality :  0.046   0.308   1632
  Planarity :  0.004   0.043   1658
  Dihedral  : 21.414 170.132   1825
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.04 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 26.79 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1080
  helix:  0.15 (0.24), residues: 456
  sheet:  1.23 (0.32), residues: 256
  loop : -1.61 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.015   0.001   TYR F  51 
 PHE   0.034   0.002   PHE B  52 
 TRP   0.013   0.002   TRP A 115 
 HIS   0.004   0.002   HIS G 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.19 (10428)
  covalent geometry    : angle       0.64755 /  0.36 (14339)
  hydrogen bonds       : bond        0.03820 /  2.49 (  517)
  hydrogen bonds       : angle       4.84085 /  3.42 ( 1423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1484.65 seconds
wall clock time: 26 minutes 24.44 seconds (1584.44 seconds total)