Starting phenix.real_space_refine
on Wed Mar  4 02:47:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sx6_55332/03_2026/9sx6_55332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sx6_55332/03_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_55332/03_2026/9sx6_55332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sx6_55332/03_2026/9sx6_55332.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sx6_55332/03_2026/9sx6_55332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sx6_55332/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.27, per 1000 atoms: 0.22
  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: 0.88
  Conformation dependent library (CDL) restraints added in 556.8 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: 1.18
  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: 1.81

  Time building geometry restraints manager: 1.19 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 1.50e-02 4.44e+03 2.81e+01
  bond pdb=" P    DA Y   6 "
       pdb=" OP2  DA Y   6 "
    ideal  model  delta    sigma   weight residual
    1.480  1.513 -0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" CG1 ILE B  30 "
       pdb=" CD1 ILE B  30 "
    ideal  model  delta    sigma   weight residual
    1.513  1.453  0.060 3.90e-02 6.57e+02 2.38e+00
  bond pdb=" P    DA Y   6 "
       pdb=" OP1  DA Y   6 "
    ideal  model  delta    sigma   weight residual
    1.480  1.507 -0.027 2.00e-02 2.50e+03 1.81e+00
  bond pdb=" C3'  DT Z  11 "
       pdb=" O3'  DT Z  11 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.46e+00
  ... (remaining 10423 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 14262
        3.45 -     6.91: 72
        6.91 -    10.36: 3
       10.36 -    13.82: 0
       13.82 -    17.27: 2
  Bond angle restraints: 14339
  Sorted by residual:
  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=" C3'  DT Z  -6 "
        pdb=" O3'  DT Z  -6 "
        pdb=" P    DT Z  -5 "
      ideal   model   delta    sigma   weight residual
     120.20  112.41    7.79 1.50e+00 4.44e-01 2.69e+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=" CA  GLU D  80 "
        pdb=" CB  GLU D  80 "
        pdb=" CG  GLU D  80 "
      ideal   model   delta    sigma   weight residual
     114.10  121.05   -6.95 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" CB  LYS A 101 "
        pdb=" CG  LYS A 101 "
        pdb=" CD  LYS A 101 "
      ideal   model   delta    sigma   weight residual
     111.30  118.38   -7.08 2.30e+00 1.89e-01 9.48e+00
  ... (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 -    0.114: 1582
       0.114 -    0.228: 49
       0.228 -    0.341: 0
       0.341 -    0.455: 0
       0.455 -    0.569: 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       2.35   -2.91   -0.57 2.00e-01 2.50e+01 8.09e+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=" CA  ASP G 100 "
            pdb=" N   ASP G 100 "
            pdb=" C   ASP G 100 "
            pdb=" CB  ASP G 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.22e-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:             4.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.760
  Find NCS groups from input model:        0.160
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  10428  Z= 0.184
  Angle     :  0.710  17.271  14339  Z= 0.391
  Chirality :  0.047   0.569   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
  covalent geometry    : bond        0.00409 (10428)
  covalent geometry    : angle       0.71026 (14339)
  hydrogen bonds       : bond        0.12576 (  517)
  hydrogen bonds       : angle       5.87953 ( 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  : 0.319 
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: 0.1051
  time to fit residues: 39.7189
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  : 0.313 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.7992

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A  56 ASN
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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
G 122 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.055129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.042043 restraints weight = 45068.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.043339 restraints weight = 22416.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.044234 restraints weight = 14323.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.044814 restraints weight = 10535.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.045124 restraints weight = 8544.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10428  Z= 0.212
  Angle     :  0.640   7.604  14339  Z= 0.356
  Chirality :  0.045   0.168   1632
  Planarity :  0.004   0.038   1658
  Dihedral  : 21.316 160.302   1839
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  7.22 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.02 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.26), residues: 1080
  helix:  0.13 (0.24), residues: 464
  sheet:  0.92 (0.31), residues: 304
  loop : -1.49 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  23 
 TYR   0.013   0.001   TYR B 120 
 PHE   0.023   0.002   PHE H  52 
 TRP   0.014   0.003   TRP H 115 
 HIS   0.004   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (10428)
  covalent geometry    : angle       0.64034 (14339)
  hydrogen bonds       : bond        0.04424 (  517)
  hydrogen bonds       : angle       5.15707 ( 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
  227 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 174
  time to evaluate  : 0.337 
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   49 GLU cc_start: 0.8486 (mp0) cc_final: 0.8282 (mp0)
REVERT: A   51 TYR cc_start: 0.9248 (t80) cc_final: 0.9039 (t80)
REVERT: A   85 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8010 (m-40)
REVERT: C   33 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8160 (p0)
REVERT: C   49 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: C   53 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8412 (mm110)
REVERT: C   69 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8908 (mtmm)
REVERT: C  113 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6814 (mt-10)
REVERT: B   49 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: B   62 GLN cc_start: 0.8180 (mp10) cc_final: 0.7971 (mp10)
REVERT: B   95 SER cc_start: 0.8961 (t) cc_final: 0.8704 (p)
REVERT: B  122 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8563 (tp-100)
REVERT: E   49 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: E   88 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7908 (pp)
REVERT: D   37 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8650 (mp0)
REVERT: D   49 GLU cc_start: 0.8736 (tp30) cc_final: 0.8410 (tp30)
REVERT: G   49 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: G  121 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8651 (mm-30)
REVERT: F   49 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: F   51 TYR cc_start: 0.9305 (t80) cc_final: 0.9098 (t80)
REVERT: F   80 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7510 (mm-30)
  outliers start: 53
  outliers final: 23
  residues processed: 213
  average time/residue: 0.0942
  time to fit residues: 28.7583
Evaluate side-chains
  176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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   50 SER
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain H residue  126 SER
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   93 LEU
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   37 GLU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  106 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 G residue  121 GLU
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:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 100 optimal weight:    0.1980
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0470
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A  85 ASN
A 108 GLN
C  33 ASN
C  38 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 GLN
G 122 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.056226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.043282 restraints weight = 45490.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.044585 restraints weight = 22903.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.045459 restraints weight = 14702.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.046063 restraints weight = 10866.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.046446 restraints weight = 8829.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10428  Z= 0.133
  Angle     :  0.583   7.924  14339  Z= 0.324
  Chirality :  0.043   0.159   1632
  Planarity :  0.003   0.038   1658
  Dihedral  : 21.181 161.280   1829
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.67 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 23.71 %
    Favored  : 72.62 %
  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: -0.03 (0.27), residues: 1080
  helix:  0.31 (0.24), residues: 464
  sheet:  1.05 (0.32), residues: 304
  loop : -1.51 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  23 
 TYR   0.012   0.001   TYR B 120 
 PHE   0.021   0.001   PHE C  58 
 TRP   0.012   0.002   TRP A 115 
 HIS   0.004   0.002   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10428)
  covalent geometry    : angle       0.58253 (14339)
  hydrogen bonds       : bond        0.03391 (  517)
  hydrogen bonds       : angle       4.76542 ( 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
  217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 0.374 
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   85 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7973 (m-40)
REVERT: C   33 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8142 (p0)
REVERT: C   49 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: C   69 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8858 (mtmm)
REVERT: C  113 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6991 (mt-10)
REVERT: B   49 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: B   52 PHE cc_start: 0.9071 (t80) cc_final: 0.8848 (t80)
REVERT: B   53 GLN cc_start: 0.9316 (mm-40) cc_final: 0.9088 (mm-40)
REVERT: B   62 GLN cc_start: 0.8152 (mp10) cc_final: 0.7802 (mp10)
REVERT: B   95 SER cc_start: 0.8847 (t) cc_final: 0.8564 (p)
REVERT: B  122 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8402 (tp-100)
REVERT: E   34 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7482 (tmt90)
REVERT: E   49 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: D   49 GLU cc_start: 0.8770 (tp30) cc_final: 0.8080 (tp30)
REVERT: D   53 GLN cc_start: 0.9372 (mm-40) cc_final: 0.8898 (mm-40)
REVERT: G   49 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: G  101 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8758 (tptp)
REVERT: G  108 GLN cc_start: 0.7808 (mp10) cc_final: 0.7539 (mp10)
REVERT: F   49 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: F   53 GLN cc_start: 0.9372 (mm-40) cc_final: 0.9024 (mm-40)
REVERT: F   80 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7499 (mm-30)
  outliers start: 37
  outliers final: 21
  residues processed: 209
  average time/residue: 0.0951
  time to fit residues: 28.2025
Evaluate side-chains
  177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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 H residue   99 LEU
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   11 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   33 ASN
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   93 LEU
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain D residue   56 ASN
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.8762

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A 119 GLN
C  33 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 122 GLN
F  14 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.056014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.042617 restraints weight = 44386.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.043892 restraints weight = 22445.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.044817 restraints weight = 14558.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.045404 restraints weight = 10734.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.045763 restraints weight = 8776.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2795

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= 0.146
  Angle     :  0.581   7.909  14339  Z= 0.323
  Chirality :  0.043   0.159   1632
  Planarity :  0.004   0.037   1658
  Dihedral  : 21.086 161.642   1829
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.85 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.31 %
    Favored  : 73.12 %
  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: -0.01 (0.26), residues: 1080
  helix:  0.33 (0.24), residues: 464
  sheet:  1.57 (0.33), residues: 256
  loop : -1.62 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  43 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.019   0.001   PHE D  52 
 TRP   0.011   0.002   TRP A 115 
 HIS   0.004   0.002   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10428)
  covalent geometry    : angle       0.58134 (14339)
  hydrogen bonds       : bond        0.03368 (  517)
  hydrogen bonds       : angle       4.67156 ( 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
  205 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.367 
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  100 ASP cc_start: 0.8580 (p0) cc_final: 0.8358 (p0)
REVERT: A  101 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8798 (mmmt)
REVERT: C   27 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8548 (p0)
REVERT: C   33 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7859 (p0)
REVERT: C   49 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8431 (tm-30)
REVERT: C   69 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8817 (mtmm)
REVERT: C  113 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7070 (mt-10)
REVERT: B   49 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: B   53 GLN cc_start: 0.9354 (mm-40) cc_final: 0.9113 (mm-40)
REVERT: B   62 GLN cc_start: 0.8274 (mp10) cc_final: 0.7763 (mp10)
REVERT: B   95 SER cc_start: 0.8785 (t) cc_final: 0.8543 (p)
REVERT: B  122 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8368 (tp-100)
REVERT: E   49 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: D   49 GLU cc_start: 0.8791 (tp30) cc_final: 0.8238 (tp30)
REVERT: D   53 GLN cc_start: 0.9375 (mm-40) cc_final: 0.9171 (mm-40)
REVERT: G    9 THR cc_start: 0.8547 (p) cc_final: 0.8270 (p)
REVERT: G   49 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: G   53 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8448 (mm110)
REVERT: G  101 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8578 (tptp)
REVERT: F   41 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7645 (mt-10)
REVERT: F   49 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8349 (tm-30)
REVERT: F   80 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7613 (mm-30)
REVERT: F  122 GLN cc_start: 0.8776 (mp10) cc_final: 0.8399 (mp10)
  outliers start: 36
  outliers final: 24
  residues processed: 194
  average time/residue: 0.0940
  time to fit residues: 25.9926
Evaluate side-chains
  176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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 H residue   24 SER
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 C residue   11 ASP
Chi-restraints excluded: chain C residue   27 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   33 ASN
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   93 LEU
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain G residue   56 ASN
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:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 105 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.056338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.043153 restraints weight = 44500.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.044439 restraints weight = 22018.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045373 restraints weight = 14052.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.045970 restraints weight = 10250.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.046377 restraints weight = 8277.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2960

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= 0.169
  Angle     :  0.579   8.016  14339  Z= 0.320
  Chirality :  0.043   0.197   1632
  Planarity :  0.004   0.040   1658
  Dihedral  : 21.018 162.173   1825
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.04 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.71 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.26), residues: 1080
  helix:  0.40 (0.24), residues: 464
  sheet:  1.53 (0.33), residues: 256
  loop : -1.56 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  66 
 TYR   0.018   0.001   TYR F  51 
 PHE   0.025   0.001   PHE B  52 
 TRP   0.011   0.002   TRP B 115 
 HIS   0.004   0.001   HIS G 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (10428)
  covalent geometry    : angle       0.57921 (14339)
  hydrogen bonds       : bond        0.03486 (  517)
  hydrogen bonds       : angle       4.69053 ( 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
  208 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 165
  time to evaluate  : 0.295 
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: H  121 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8393 (mp0)
REVERT: C   27 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8490 (p0)
REVERT: C   28 SER cc_start: 0.8753 (t) cc_final: 0.8522 (p)
REVERT: C   33 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7872 (p0)
REVERT: C   49 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8470 (tm-30)
REVERT: C   69 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8766 (mtmm)
REVERT: C  113 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7184 (mt-10)
REVERT: B   49 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8224 (tm-30)
REVERT: B   62 GLN cc_start: 0.8351 (mp10) cc_final: 0.7701 (mp10)
REVERT: B   95 SER cc_start: 0.8878 (t) cc_final: 0.8609 (p)
REVERT: B  122 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8391 (tp-100)
REVERT: E   34 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7763 (tmt90)
REVERT: E   49 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: D   49 GLU cc_start: 0.8840 (tp30) cc_final: 0.8313 (tp30)
REVERT: D  100 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7743 (p0)
REVERT: D  101 LYS cc_start: 0.9053 (mppt) cc_final: 0.8729 (mmmm)
REVERT: G   49 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8078 (tm-30)
REVERT: G   53 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8583 (mm110)
REVERT: G  101 LYS cc_start: 0.9300 (mmmm) cc_final: 0.8464 (tptp)
REVERT: F   41 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7663 (mt-10)
REVERT: F   49 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: F   80 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: F  122 GLN cc_start: 0.8850 (mp10) cc_final: 0.8485 (mp10)
  outliers start: 43
  outliers final: 28
  residues processed: 195
  average time/residue: 0.0942
  time to fit residues: 26.1000
Evaluate side-chains
  182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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 H residue   24 SER
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   27 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   33 ASN
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   93 LEU
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    9 THR
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   81 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   54 THR
Chi-restraints excluded: chain G residue   56 ASN
Chi-restraints excluded: chain F residue  103 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 122 GLN
G  38 ASN
G 108 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.056365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.043097 restraints weight = 44710.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.044403 restraints weight = 22018.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045335 restraints weight = 14012.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.045921 restraints weight = 10237.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.046334 restraints weight = 8297.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3141

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= 0.146
  Angle     :  0.583   8.103  14339  Z= 0.320
  Chirality :  0.043   0.169   1632
  Planarity :  0.004   0.038   1658
  Dihedral  : 20.974 162.806   1825
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.85 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 24.40 %
    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:  0.16 (0.27), residues: 1080
  helix:  0.46 (0.24), residues: 464
  sheet:  1.19 (0.32), residues: 288
  loop : -1.32 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  15 
 TYR   0.015   0.001   TYR F  51 
 PHE   0.022   0.001   PHE A  52 
 TRP   0.009   0.002   TRP D 115 
 HIS   0.004   0.002   HIS G 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10428)
  covalent geometry    : angle       0.58281 (14339)
  hydrogen bonds       : bond        0.03248 (  517)
  hydrogen bonds       : angle       4.61062 ( 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
  202 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  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: C   27 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8508 (p0)
REVERT: C   33 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7871 (p0)
REVERT: C   49 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: C   69 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8754 (mtmm)
REVERT: C  113 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: C  119 GLN cc_start: 0.9441 (mm-40) cc_final: 0.9207 (mm-40)
REVERT: B   49 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: B   95 SER cc_start: 0.8865 (t) cc_final: 0.8597 (p)
REVERT: B  122 GLN cc_start: 0.8880 (tp40) cc_final: 0.8381 (tp-100)
REVERT: E   34 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7768 (tmt90)
REVERT: E   49 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: D   49 GLU cc_start: 0.8829 (tp30) cc_final: 0.8265 (tp30)
REVERT: D  100 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7577 (p0)
REVERT: G   49 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: G   53 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8585 (mm110)
REVERT: G  101 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8540 (tptp)
REVERT: G  117 LYS cc_start: 0.9605 (tptm) cc_final: 0.9326 (tptp)
REVERT: F   41 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7672 (mt-10)
REVERT: F   49 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: F   53 GLN cc_start: 0.9473 (mm-40) cc_final: 0.9114 (mm-40)
REVERT: F  122 GLN cc_start: 0.8910 (mp10) cc_final: 0.8691 (mm-40)
  outliers start: 37
  outliers final: 25
  residues processed: 193
  average time/residue: 0.0965
  time to fit residues: 26.5696
Evaluate side-chains
  176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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 H residue   24 SER
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   27 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   33 ASN
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   93 LEU
Chi-restraints excluded: chain B residue   55 PHE
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   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN
G 108 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.055790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.042666 restraints weight = 44484.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.043936 restraints weight = 22218.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.044815 restraints weight = 14183.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.045334 restraints weight = 10444.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.045740 restraints weight = 8558.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  10428  Z= 0.204
  Angle     :  0.620   8.727  14339  Z= 0.339
  Chirality :  0.044   0.171   1632
  Planarity :  0.004   0.039   1658
  Dihedral  : 20.988 163.348   1825
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  6.94 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.70 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.01 (0.26), residues: 1080
  helix:  0.43 (0.25), residues: 456
  sheet:  1.42 (0.33), residues: 256
  loop : -1.54 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  70 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.027   0.002   PHE D  52 
 TRP   0.012   0.002   TRP B 115 
 HIS   0.003   0.001   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (10428)
  covalent geometry    : angle       0.62024 (14339)
  hydrogen bonds       : bond        0.03661 (  517)
  hydrogen bonds       : angle       4.73073 ( 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
  187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.489 
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  136 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8759 (mtp180)
REVERT: H   86 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8395 (mtp85)
REVERT: H  121 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8408 (mp0)
REVERT: C   27 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8486 (p0)
REVERT: C   33 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8039 (p0)
REVERT: C   49 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8473 (tm-30)
REVERT: C   69 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8788 (mtmm)
REVERT: C  113 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7345 (mt-10)
REVERT: C  119 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9218 (mm-40)
REVERT: B   49 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: B   95 SER cc_start: 0.8821 (t) cc_final: 0.8551 (p)
REVERT: B  122 GLN cc_start: 0.8910 (tp40) cc_final: 0.8517 (tp-100)
REVERT: E   34 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7828 (tmt90)
REVERT: E   49 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: D   49 GLU cc_start: 0.8831 (tp30) cc_final: 0.8181 (tp30)
REVERT: D   53 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8972 (mm-40)
REVERT: G   49 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: G  101 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8673 (tptp)
REVERT: F   41 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7672 (mt-10)
REVERT: F   49 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8466 (tm-30)
REVERT: F  122 GLN cc_start: 0.8932 (mp10) cc_final: 0.8642 (mp10)
  outliers start: 42
  outliers final: 31
  residues processed: 181
  average time/residue: 0.0993
  time to fit residues: 25.2752
Evaluate side-chains
  175 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  136 ARG
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   86 ARG
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   33 ASN
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   93 LEU
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain B residue   55 PHE
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   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain D residue   56 ASN
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  106 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
** 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 = 0.3322 r_free = 0.3322 target = 0.055591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.042102 restraints weight = 44482.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.043412 restraints weight = 22107.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044302 restraints weight = 14124.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.044927 restraints weight = 10471.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.045313 restraints weight = 8492.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10428  Z= 0.157
  Angle     :  0.606   6.939  14339  Z= 0.333
  Chirality :  0.044   0.205   1632
  Planarity :  0.004   0.038   1658
  Dihedral  : 20.974 164.126   1825
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  6.30 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 25.40 %
    Favored  : 70.93 %
  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:  0.15 (0.27), residues: 1080
  helix:  0.54 (0.25), residues: 448
  sheet:  1.09 (0.31), residues: 296
  loop : -1.36 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.025   0.001   PHE A  52 
 TRP   0.010   0.002   TRP B 115 
 HIS   0.004   0.002   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (10428)
  covalent geometry    : angle       0.60633 (14339)
  hydrogen bonds       : bond        0.03265 (  517)
  hydrogen bonds       : angle       4.62394 ( 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
  189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 152
  time to evaluate  : 0.403 
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: H   86 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8345 (mtp85)
REVERT: H  121 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8370 (mp0)
REVERT: C   49 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8447 (tm-30)
REVERT: C   69 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8817 (mtmm)
REVERT: C  113 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7316 (mt-10)
REVERT: C  119 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9184 (mm-40)
REVERT: B   49 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: B   95 SER cc_start: 0.8775 (t) cc_final: 0.8522 (p)
REVERT: B  122 GLN cc_start: 0.8876 (tp40) cc_final: 0.8523 (tp-100)
REVERT: E   34 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7793 (tmt90)
REVERT: E   49 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: D   49 GLU cc_start: 0.8783 (tp30) cc_final: 0.8149 (tp30)
REVERT: D   53 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8957 (mm-40)
REVERT: D  101 LYS cc_start: 0.9352 (mmmt) cc_final: 0.9148 (mmmt)
REVERT: G   49 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: G  101 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8628 (tptp)
REVERT: F   41 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7662 (mt-10)
REVERT: F   49 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: F   53 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9112 (mm-40)
REVERT: F   55 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8701 (t80)
REVERT: F  122 GLN cc_start: 0.8927 (mp10) cc_final: 0.8706 (mp10)
  outliers start: 37
  outliers final: 27
  residues processed: 181
  average time/residue: 0.0956
  time to fit residues: 24.5792
Evaluate side-chains
  175 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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 H residue   24 SER
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   86 ARG
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   32 ILE
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   93 LEU
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   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain D residue   56 ASN
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  106 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
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**
** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.055802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.042005 restraints weight = 44712.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.043281 restraints weight = 22954.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.044135 restraints weight = 14966.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.044758 restraints weight = 11236.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.045188 restraints weight = 9112.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10428  Z= 0.193
  Angle     :  0.621   6.688  14339  Z= 0.340
  Chirality :  0.044   0.191   1632
  Planarity :  0.004   0.040   1658
  Dihedral  : 20.980 164.721   1825
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.04 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.50 %
    Favored  : 71.03 %
  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:  0.09 (0.27), residues: 1080
  helix:  0.51 (0.25), residues: 448
  sheet:  1.02 (0.31), residues: 296
  loop : -1.38 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.011   0.001   TYR B 120 
 PHE   0.024   0.001   PHE D  52 
 TRP   0.011   0.002   TRP B 115 
 HIS   0.003   0.001   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (10428)
  covalent geometry    : angle       0.62122 (14339)
  hydrogen bonds       : bond        0.03575 (  517)
  hydrogen bonds       : angle       4.69919 ( 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
  180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8765 (mtp180)
REVERT: H   86 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8375 (mtp85)
REVERT: C   49 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: C   69 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8792 (mtmm)
REVERT: C  113 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7061 (mt-10)
REVERT: C  119 GLN cc_start: 0.9457 (mm-40) cc_final: 0.9209 (mm-40)
REVERT: B   49 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8246 (tm-30)
REVERT: B   95 SER cc_start: 0.8789 (t) cc_final: 0.8532 (p)
REVERT: B  122 GLN cc_start: 0.8921 (tp40) cc_final: 0.8564 (tp-100)
REVERT: E   34 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7789 (tmt90)
REVERT: E   49 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8318 (tm-30)
REVERT: D   49 GLU cc_start: 0.8826 (tp30) cc_final: 0.8190 (tp30)
REVERT: D   53 GLN cc_start: 0.9350 (mm-40) cc_final: 0.9008 (mm-40)
REVERT: D  101 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9151 (mmmt)
REVERT: G   49 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: F   41 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: F   49 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: F   53 GLN cc_start: 0.9466 (mm-40) cc_final: 0.9152 (mm-40)
REVERT: F   55 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8669 (t80)
  outliers start: 35
  outliers final: 28
  residues processed: 174
  average time/residue: 0.1033
  time to fit residues: 25.2652
Evaluate side-chains
  176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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  136 ARG
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   86 ARG
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   72 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain B residue   55 PHE
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   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain D residue   56 ASN
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
Chi-restraints excluded: chain F residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.3186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.053731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.040337 restraints weight = 43959.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.041583 restraints weight = 21784.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.042422 restraints weight = 13936.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.043005 restraints weight = 10365.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.043412 restraints weight = 8462.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  10428  Z= 0.252
  Angle     :  0.663   7.658  14339  Z= 0.361
  Chirality :  0.045   0.192   1632
  Planarity :  0.004   0.042   1658
  Dihedral  : 21.073 165.589   1825
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.04 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.69 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.26), residues: 1080
  helix:  0.35 (0.25), residues: 456
  sheet:  1.17 (0.32), residues: 256
  loop : -1.62 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  70 
 TYR   0.012   0.001   TYR B 120 
 PHE   0.027   0.002   PHE D  52 
 TRP   0.014   0.002   TRP B 115 
 HIS   0.004   0.001   HIS F 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 (10428)
  covalent geometry    : angle       0.66263 (14339)
  hydrogen bonds       : bond        0.04152 (  517)
  hydrogen bonds       : angle       4.88067 ( 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
  173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8716 (mtp180)
REVERT: H   27 ASP cc_start: 0.8187 (p0) cc_final: 0.7812 (p0)
REVERT: H   86 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8336 (mtp85)
REVERT: C   27 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8619 (p0)
REVERT: C   49 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8500 (tm-30)
REVERT: C   69 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8823 (mtmm)
REVERT: C  113 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7443 (mt-10)
REVERT: C  119 GLN cc_start: 0.9467 (mm-40) cc_final: 0.9218 (mm-40)
REVERT: B   49 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8305 (tm-30)
REVERT: B   95 SER cc_start: 0.8799 (t) cc_final: 0.8545 (p)
REVERT: B  122 GLN cc_start: 0.8896 (tp40) cc_final: 0.8555 (tp-100)
REVERT: E   34 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7796 (tmt90)
REVERT: E   49 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8310 (tm-30)
REVERT: D   49 GLU cc_start: 0.8833 (tp30) cc_final: 0.8204 (tp30)
REVERT: D   53 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8933 (mm-40)
REVERT: D  101 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9120 (mmmt)
REVERT: G   49 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: F   41 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7708 (mt-10)
REVERT: F   49 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: F   55 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8692 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 168
  average time/residue: 0.0928
  time to fit residues: 22.3304
Evaluate side-chains
  167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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   72 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   86 ARG
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   69 LYS
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain B residue   55 PHE
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   27 ASP
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain D residue   56 ASN
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:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 GLN
** 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 = 0.3328 r_free = 0.3328 target = 0.055534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.042074 restraints weight = 43950.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.043336 restraints weight = 21994.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.044236 restraints weight = 14102.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.044806 restraints weight = 10415.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.045225 restraints weight = 8476.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10428  Z= 0.153
  Angle     :  0.621   7.752  14339  Z= 0.341
  Chirality :  0.044   0.186   1632
  Planarity :  0.003   0.038   1658
  Dihedral  : 20.989 167.192   1823
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  6.20 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 26.39 %
    Favored  : 70.63 %
  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: -0.02 (0.27), residues: 1080
  helix:  0.43 (0.25), residues: 456
  sheet:  0.92 (0.32), residues: 288
  loop : -1.40 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  70 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.025   0.001   PHE C  58 
 TRP   0.010   0.002   TRP D 115 
 HIS   0.004   0.002   HIS G 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10428)
  covalent geometry    : angle       0.62144 (14339)
  hydrogen bonds       : bond        0.03254 (  517)
  hydrogen bonds       : angle       4.66026 ( 1423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1576.78 seconds
wall clock time: 27 minutes 57.92 seconds (1677.92 seconds total)