Starting phenix.real_space_refine
on Sat Aug 23 16:19:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hwz_35069/08_2025/8hwz_35069.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hwz_35069/08_2025/8hwz_35069.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hwz_35069/08_2025/8hwz_35069.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hwz_35069/08_2025/8hwz_35069.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hwz_35069/08_2025/8hwz_35069.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hwz_35069/08_2025/8hwz_35069.cif"
  }
  resolution = 3.56
  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=   0.003 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    8453      2.51       5
     N    2432      2.21       5
     O    2728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13625
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "B"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 1131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1131
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 140}
    Chain: "D"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1130
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "G"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "I"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "K"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1130
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "H"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "J"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "L"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1130
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 3.89, per 1000 atoms: 0.29
  Number of scatterers: 13625
  At special positions: 0
  Unit cell: (103.04, 103.04, 102.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O    2728      8.00
     N    2432      7.00
     C    8453      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 632.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3310

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 0 sheets defined
      83.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 44
    Processing helix  chain 'A' and resid 48 through 77
    Processing helix  chain 'A' and resid 84 through 92
    Processing helix  chain 'A' and resid 103 through 133
      removed outlier: 4.001A  pdb=" N   ASP A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   ALA A 128 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 156
    Processing helix  chain 'B' and resid 17 through 44
    Processing helix  chain 'B' and resid 48 through 77
      removed outlier: 3.914A  pdb=" N   LEU B  52 " --> pdb=" O   ASN B  48 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP B  57 " --> pdb=" O   HIS B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 92
    Processing helix  chain 'B' and resid 103 through 131
      removed outlier: 4.464A  pdb=" N   ASP B 127 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA B 128 " --> pdb=" O   ARG B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 156
    Processing helix  chain 'C' and resid 18 through 44
    Processing helix  chain 'C' and resid 48 through 77
    Processing helix  chain 'C' and resid 84 through 92
    Processing helix  chain 'C' and resid 103 through 133
      removed outlier: 4.348A  pdb=" N   ASP C 127 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   ALA C 128 " --> pdb=" O   ARG C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 156
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'D' and resid 17 through 44
      removed outlier: 3.554A  pdb=" N   VAL D  26 " --> pdb=" O   ASN D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 77
      removed outlier: 3.858A  pdb=" N   LEU D  52 " --> pdb=" O   ASN D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 92
    Processing helix  chain 'D' and resid 103 through 133
      removed outlier: 4.064A  pdb=" N   ASP D 127 " --> pdb=" O   ARG D 123 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   ALA D 128 " --> pdb=" O   ARG D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 133 through 156
    Processing helix  chain 'E' and resid 17 through 44
    Processing helix  chain 'E' and resid 48 through 77
    Processing helix  chain 'E' and resid 84 through 92
    Processing helix  chain 'E' and resid 103 through 133
      removed outlier: 4.058A  pdb=" N   ASP E 127 " --> pdb=" O   ARG E 123 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ALA E 128 " --> pdb=" O   ARG E 124 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 133 through 156
    Processing helix  chain 'G' and resid 17 through 44
    Processing helix  chain 'G' and resid 48 through 77
      removed outlier: 3.911A  pdb=" N   LEU G  52 " --> pdb=" O   ASN G  48 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASP G  57 " --> pdb=" O   HIS G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 84 through 92
    Processing helix  chain 'G' and resid 103 through 131
      removed outlier: 4.413A  pdb=" N   ASP G 127 " --> pdb=" O   ARG G 123 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   ALA G 128 " --> pdb=" O   ARG G 124 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 133 through 159
      removed outlier: 4.079A  pdb=" N   GLU G 157 " --> pdb=" O   LEU G 153 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASN G 158 " --> pdb=" O   ILE G 154 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 17 through 44
    Processing helix  chain 'I' and resid 48 through 77
    Processing helix  chain 'I' and resid 84 through 92
    Processing helix  chain 'I' and resid 103 through 133
      removed outlier: 4.489A  pdb=" N   ASP I 127 " --> pdb=" O   ARG I 123 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   ALA I 128 " --> pdb=" O   ARG I 124 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 133 through 156
    Processing helix  chain 'K' and resid 17 through 43
    Processing helix  chain 'K' and resid 48 through 77
      removed outlier: 3.873A  pdb=" N   LEU K  52 " --> pdb=" O   ASN K  48 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 92
    Processing helix  chain 'K' and resid 103 through 133
      removed outlier: 4.219A  pdb=" N   ASP K 127 " --> pdb=" O   ARG K 123 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ALA K 128 " --> pdb=" O   ARG K 124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 133 through 156
    Processing helix  chain 'F' and resid 17 through 44
    Processing helix  chain 'F' and resid 48 through 77
    Processing helix  chain 'F' and resid 84 through 92
    Processing helix  chain 'F' and resid 103 through 133
      removed outlier: 4.040A  pdb=" N   ASP F 127 " --> pdb=" O   ARG F 123 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ALA F 128 " --> pdb=" O   ARG F 124 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 133 through 156
    Processing helix  chain 'H' and resid 17 through 44
    Processing helix  chain 'H' and resid 48 through 77
      removed outlier: 4.003A  pdb=" N   LEU H  52 " --> pdb=" O   ASN H  48 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP H  57 " --> pdb=" O   HIS H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 84 through 92
    Processing helix  chain 'H' and resid 103 through 131
      removed outlier: 4.615A  pdb=" N   ASP H 127 " --> pdb=" O   ARG H 123 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   ALA H 128 " --> pdb=" O   ARG H 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 133 through 156
    Processing helix  chain 'J' and resid 17 through 44
    Processing helix  chain 'J' and resid 48 through 77
    Processing helix  chain 'J' and resid 84 through 92
    Processing helix  chain 'J' and resid 103 through 133
      removed outlier: 4.529A  pdb=" N   ASP J 127 " --> pdb=" O   ARG J 123 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ALA J 128 " --> pdb=" O   ARG J 124 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 133 through 156
    Processing helix  chain 'J' and resid 157 through 159
      No H-bonds generated for 'chain 'J' and resid 157 through 159'
    Processing helix  chain 'L' and resid 17 through 44
    Processing helix  chain 'L' and resid 48 through 77
      removed outlier: 3.848A  pdb=" N   LEU L  52 " --> pdb=" O   ASN L  48 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 84 through 92
    Processing helix  chain 'L' and resid 103 through 133
      removed outlier: 4.170A  pdb=" N   ASP L 127 " --> pdb=" O   ARG L 123 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ALA L 128 " --> pdb=" O   ARG L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 133 through 159
      removed outlier: 4.114A  pdb=" N   GLU L 157 " --> pdb=" O   LEU L 153 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ASN L 158 " --> pdb=" O   ILE L 154 " (cutoff:3.500A)

    1185 hydrogen bonds defined for protein.
    3555 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4833
        1.34 -     1.45: 1063
        1.45 -     1.57: 7909
        1.57 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 13829
  Sorted by residual:
  bond pdb=" CB  PRO F  98 "
       pdb=" CG  PRO F  98 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.08e+00
  bond pdb=" CB  MET C  74 "
       pdb=" CG  MET C  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.20e-01
  bond pdb=" CB  GLN D  36 "
       pdb=" CG  GLN D  36 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.55e-01
  bond pdb=" C   VAL A 125 "
       pdb=" O   VAL A 125 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.35e-02 5.49e+03 8.01e-01
  bond pdb=" CA  THR F  16 "
       pdb=" C   THR F  16 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.10e-02 2.27e+03 7.99e-01
  ... (remaining 13824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 18464
        1.99 -     3.97: 340
        3.97 -     5.96: 21
        5.96 -     7.94: 0
        7.94 -     9.93: 1
  Bond angle restraints: 18826
  Sorted by residual:
  angle pdb=" N   GLY B  46 "
        pdb=" CA  GLY B  46 "
        pdb=" C   GLY B  46 "
      ideal   model   delta    sigma   weight residual
     110.43  114.48   -4.05 1.35e+00 5.49e-01 9.00e+00
  angle pdb=" N   ARG H 124 "
        pdb=" CA  ARG H 124 "
        pdb=" CB  ARG H 124 "
      ideal   model   delta    sigma   weight residual
     110.01  114.17   -4.16 1.45e+00 4.76e-01 8.24e+00
  angle pdb=" N   HIS B 126 "
        pdb=" CA  HIS B 126 "
        pdb=" C   HIS B 126 "
      ideal   model   delta    sigma   weight residual
     111.07  114.08   -3.01 1.07e+00 8.73e-01 7.91e+00
  angle pdb=" N   HIS G 126 "
        pdb=" CA  HIS G 126 "
        pdb=" C   HIS G 126 "
      ideal   model   delta    sigma   weight residual
     111.28  114.19   -2.91 1.09e+00 8.42e-01 7.11e+00
  angle pdb=" N   VAL I  80 "
        pdb=" CA  VAL I  80 "
        pdb=" C   VAL I  80 "
      ideal   model   delta    sigma   weight residual
     107.89  110.79   -2.90 1.09e+00 8.42e-01 7.08e+00
  ... (remaining 18821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7545
       17.92 -    35.83: 663
       35.83 -    53.75: 118
       53.75 -    71.67: 27
       71.67 -    89.58: 22
  Dihedral angle restraints: 8375
    sinusoidal: 3326
      harmonic: 5049
  Sorted by residual:
  dihedral pdb=" CA  TRP I  42 "
           pdb=" C   TRP I  42 "
           pdb=" N   ASN I  43 "
           pdb=" CA  ASN I  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  TRP C  42 "
           pdb=" C   TRP C  42 "
           pdb=" N   ASN C  43 "
           pdb=" CA  ASN C  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.70  -17.30     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP K  86 "
           pdb=" CB  ASP K  86 "
           pdb=" CG  ASP K  86 "
           pdb=" OD1 ASP K  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.46   59.46     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 8372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1316
       0.026 -    0.051: 586
       0.051 -    0.077: 245
       0.077 -    0.102: 67
       0.102 -    0.128: 28
  Chirality restraints: 2242
  Sorted by residual:
  chirality pdb=" CA  VAL F  45 "
            pdb=" N   VAL F  45 "
            pdb=" C   VAL F  45 "
            pdb=" CB  VAL F  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CB  VAL B 125 "
            pdb=" CA  VAL B 125 "
            pdb=" CG1 VAL B 125 "
            pdb=" CG2 VAL B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ASP A 145 "
            pdb=" N   ASP A 145 "
            pdb=" C   ASP A 145 "
            pdb=" CB  ASP A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 2239 not shown)

  Planarity restraints: 2503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  97 "   -0.064 5.00e-02 4.00e+02   9.70e-02 1.51e+01
        pdb=" N   PRO B  98 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO B  98 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B  98 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F  97 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.04e+01
        pdb=" N   PRO F  98 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO F  98 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO F  98 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE G  97 "   -0.045 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO G  98 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO G  98 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G  98 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 2500 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 167
        2.66 -     3.22: 14222
        3.22 -     3.78: 22863
        3.78 -     4.34: 27347
        4.34 -     4.90: 47587
  Nonbonded interactions: 112186
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K  39 "
            pdb=" ND2 ASN K  43 "
     model   vdw
     2.103 3.120
  nonbonded pdb=" OD2 ASP H 120 "
            pdb=" NH1 ARG H 124 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" OD2 ASP B 133 "
            pdb=" OG  SER B 135 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   GLU A  18 "
            pdb=" ND2 ASN A  22 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD2 ASP C  68 "
            pdb=" NZ  LYS D  38 "
     model   vdw
     2.241 3.120
  ... (remaining 112181 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' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'B' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'C' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'D' and resid 17 through 161)
  selection = (chain 'E' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'F' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'G' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'H' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'I' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'J' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'K' and resid 17 through 161)
  selection = (chain 'L' and resid 17 through 161)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.750
  Find NCS groups from input model:        0.340
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
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      :  0.003   0.052  13829  Z= 0.152
  Angle     :  0.620   9.930  18826  Z= 0.365
  Chirality :  0.036   0.128   2242
  Planarity :  0.005   0.097   2503
  Dihedral  : 14.516  89.585   5065
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  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 aren not related in a simple way.
  whole:  4.47 (0.20), residues: 1727
  helix:  3.41 (0.13), residues: 1417
  sheet:  None (None), residues: 0
  loop :  0.52 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 124 
 PHE   0.024   0.002   PHE I  49 
 TRP   0.016   0.001   TRP C 152 
 HIS   0.005   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (13829)
  covalent geometry    : angle       0.61970 (18826)
  hydrogen bonds       : bond        0.09094 ( 1185)
  hydrogen bonds       : angle       3.69380 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 353
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7579 (mp0) cc_final: 0.7375 (tt0)
REVERT: B   24 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8391 (tp40)
REVERT: C   32 GLU cc_start: 0.8494 (tp30) cc_final: 0.8045 (tp30)
REVERT: C   55 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8467 (tp-100)
REVERT: D  157 GLU cc_start: 0.8809 (tp30) cc_final: 0.8474 (tp30)
REVERT: E  157 GLU cc_start: 0.8713 (tp30) cc_final: 0.8436 (tp30)
REVERT: K   22 ASN cc_start: 0.8764 (m110) cc_final: 0.8394 (m110)
REVERT: K  103 SER cc_start: 0.8739 (t) cc_final: 0.8444 (p)
REVERT: K  148 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8270 (mm-30)
REVERT: F   32 GLU cc_start: 0.8313 (tp30) cc_final: 0.8093 (tp30)
REVERT: H   55 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8121 (tp-100)
REVERT: J   32 GLU cc_start: 0.8546 (tp30) cc_final: 0.8178 (tp30)
REVERT: J   43 ASN cc_start: 0.8704 (t0) cc_final: 0.8484 (t0)
REVERT: L  120 ASP cc_start: 0.8126 (t70) cc_final: 0.7909 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 353
  average time/residue: 0.0991
  time to fit residues: 54.7734
Evaluate side-chains
  253 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0870
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A  43 ASN
A  48 ASN
A 158 ASN
B  41 HIS
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 ASN
C  36 GLN
C 158 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  22 ASN
E  36 GLN
E  43 ASN
G  41 HIS
I  43 ASN
** I  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 158 ASN
H  43 ASN
H 158 ASN
** J  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.081621 restraints weight = 31108.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.084816 restraints weight = 15285.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.086897 restraints weight = 9052.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.088459 restraints weight = 6079.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.089628 restraints weight = 4239.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13829  Z= 0.122
  Angle     :  0.516   8.954  18826  Z= 0.277
  Chirality :  0.036   0.153   2242
  Planarity :  0.005   0.072   2503
  Dihedral  :  4.430  61.833   1883
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  :  8.37 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.52 (0.20), residues: 1727
  helix:  3.46 (0.13), residues: 1417
  sheet:  None (None), residues: 0
  loop :  0.53 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG J 155 
 PHE   0.022   0.002   PHE A  19 
 TRP   0.011   0.001   TRP C 152 
 HIS   0.007   0.002   HIS L  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (13829)
  covalent geometry    : angle       0.51588 (18826)
  hydrogen bonds       : bond        0.04233 ( 1185)
  hydrogen bonds       : angle       3.32808 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 307
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 THR cc_start: 0.8050 (m) cc_final: 0.7834 (p)
REVERT: A  157 GLU cc_start: 0.8712 (tp30) cc_final: 0.8187 (tp30)
REVERT: B   24 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8184 (tp40)
REVERT: B  144 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8417 (tt)
REVERT: C   32 GLU cc_start: 0.8133 (tp30) cc_final: 0.7668 (tp30)
REVERT: C   55 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8719 (tp40)
REVERT: D   18 GLU cc_start: 0.7767 (pm20) cc_final: 0.7388 (tt0)
REVERT: D  133 ASP cc_start: 0.6882 (t0) cc_final: 0.6673 (t0)
REVERT: E   24 GLN cc_start: 0.8773 (tm-30) cc_final: 0.7912 (tp40)
REVERT: E   32 GLU cc_start: 0.8610 (tp30) cc_final: 0.8368 (tp30)
REVERT: G  133 ASP cc_start: 0.7343 (t0) cc_final: 0.6972 (t0)
REVERT: I   32 GLU cc_start: 0.8321 (tp30) cc_final: 0.7899 (tp30)
REVERT: K  103 SER cc_start: 0.8399 (t) cc_final: 0.8032 (p)
REVERT: K  133 ASP cc_start: 0.6958 (t0) cc_final: 0.6733 (t0)
REVERT: F   32 GLU cc_start: 0.8326 (tp30) cc_final: 0.7835 (tp30)
REVERT: H   18 GLU cc_start: 0.7937 (mp0) cc_final: 0.7718 (tt0)
REVERT: H   55 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8142 (tp-100)
REVERT: H  125 VAL cc_start: 0.9153 (p) cc_final: 0.8931 (p)
REVERT: J   32 GLU cc_start: 0.8407 (tp30) cc_final: 0.7999 (tp30)
REVERT: J  133 ASP cc_start: 0.6825 (t0) cc_final: 0.6515 (t0)
REVERT: J  150 GLN cc_start: 0.9306 (mm110) cc_final: 0.9069 (mm110)
REVERT: L   18 GLU cc_start: 0.7840 (pm20) cc_final: 0.7568 (tt0)
REVERT: L  148 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8149 (mm-30)
  outliers start: 51
  outliers final: 31
  residues processed: 333
  average time/residue: 0.0973
  time to fit residues: 50.7003
Evaluate side-chains
  293 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 261
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   48 ASN
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  144 ILE
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 137 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   chunk 66 optimal weight:    0.8980
   chunk 165 optimal weight:    0.9980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  24 GLN
I  48 ASN
** I  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  22 ASN
** K  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  48 ASN
** F  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  22 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.089980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.077730 restraints weight = 32175.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.080837 restraints weight = 16124.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.082905 restraints weight = 9704.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.084479 restraints weight = 6541.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.085574 restraints weight = 4630.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13829  Z= 0.144
  Angle     :  0.523   9.388  18826  Z= 0.278
  Chirality :  0.036   0.154   2242
  Planarity :  0.005   0.063   2503
  Dihedral  :  4.462  63.300   1883
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.49 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.42 (0.20), residues: 1727
  helix:  3.38 (0.13), residues: 1417
  sheet:  None (None), residues: 0
  loop :  0.54 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 114 
 PHE   0.023   0.002   PHE E  49 
 TRP   0.009   0.001   TRP H  42 
 HIS   0.006   0.002   HIS K  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (13829)
  covalent geometry    : angle       0.52270 (18826)
  hydrogen bonds       : bond        0.04353 ( 1185)
  hydrogen bonds       : angle       3.33346 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 270
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7800 (m-80) cc_final: 0.7378 (m-80)
REVERT: A  121 THR cc_start: 0.8197 (m) cc_final: 0.7959 (p)
REVERT: A  135 SER cc_start: 0.8727 (p) cc_final: 0.8516 (p)
REVERT: A  157 GLU cc_start: 0.8696 (tp30) cc_final: 0.8333 (tp30)
REVERT: B   24 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8143 (tp40)
REVERT: B   65 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8723 (mm-30)
REVERT: C  135 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8502 (p)
REVERT: D   32 GLU cc_start: 0.8317 (tp30) cc_final: 0.8088 (tp30)
REVERT: E   24 GLN cc_start: 0.8850 (tm-30) cc_final: 0.7968 (tp40)
REVERT: E   32 GLU cc_start: 0.8663 (tp30) cc_final: 0.8458 (tp30)
REVERT: E   72 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7713 (mm-30)
REVERT: G   18 GLU cc_start: 0.7620 (mp0) cc_final: 0.7378 (tt0)
REVERT: G  133 ASP cc_start: 0.7313 (t0) cc_final: 0.7036 (t0)
REVERT: I   18 GLU cc_start: 0.8467 (tt0) cc_final: 0.8207 (mp0)
REVERT: I   32 GLU cc_start: 0.8383 (tp30) cc_final: 0.7935 (tp30)
REVERT: I   55 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8524 (tp40)
REVERT: K  103 SER cc_start: 0.8441 (t) cc_final: 0.8079 (p)
REVERT: F   32 GLU cc_start: 0.8335 (tp30) cc_final: 0.7875 (tp30)
REVERT: H  103 SER cc_start: 0.8682 (t) cc_final: 0.8300 (p)
REVERT: H  120 ASP cc_start: 0.8332 (t0) cc_final: 0.7297 (t0)
REVERT: H  121 THR cc_start: 0.8381 (p) cc_final: 0.7515 (t)
REVERT: H  124 ARG cc_start: 0.7904 (mpp-170) cc_final: 0.7222 (mtm110)
REVERT: J   18 GLU cc_start: 0.8007 (mp0) cc_final: 0.7715 (tt0)
REVERT: J   43 ASN cc_start: 0.8627 (t0) cc_final: 0.8331 (t0)
REVERT: J  133 ASP cc_start: 0.6782 (t0) cc_final: 0.6568 (t0)
REVERT: L  148 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8115 (mm-30)
  outliers start: 47
  outliers final: 37
  residues processed: 300
  average time/residue: 0.0995
  time to fit residues: 46.9979
Evaluate side-chains
  289 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 251
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 157 optimal weight:    9.9990
   chunk 96 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 161 optimal weight:    4.9990
   chunk 136 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 167 optimal weight:    0.8980
   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  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  43 ASN
K  39 GLN
K  48 ASN
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  22 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.093454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.081900 restraints weight = 31429.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.084902 restraints weight = 15618.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.087027 restraints weight = 9294.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.088434 restraints weight = 6137.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089502 restraints weight = 4345.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13829  Z= 0.121
  Angle     :  0.495   9.544  18826  Z= 0.262
  Chirality :  0.035   0.152   2242
  Planarity :  0.004   0.058   2503
  Dihedral  :  4.435  65.132   1883
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 13.84 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.50 (0.20), residues: 1727
  helix:  3.43 (0.13), residues: 1417
  sheet:  None (None), residues: 0
  loop :  0.56 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 114 
 PHE   0.018   0.002   PHE H  49 
 TRP   0.009   0.001   TRP B 152 
 HIS   0.006   0.002   HIS K  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (13829)
  covalent geometry    : angle       0.49520 (18826)
  hydrogen bonds       : bond        0.04074 ( 1185)
  hydrogen bonds       : angle       3.23613 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 294
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8885 (tp40) cc_final: 0.8542 (tp40)
REVERT: A  100 PHE cc_start: 0.7696 (m-80) cc_final: 0.7328 (m-80)
REVERT: A  121 THR cc_start: 0.8245 (m) cc_final: 0.7995 (p)
REVERT: A  157 GLU cc_start: 0.8596 (tp30) cc_final: 0.8277 (tp30)
REVERT: B   24 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8055 (tp40)
REVERT: B   65 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8689 (mm-30)
REVERT: B  144 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8663 (tt)
REVERT: C   32 GLU cc_start: 0.7994 (tp30) cc_final: 0.7555 (tp30)
REVERT: C   36 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8688 (mm-40)
REVERT: C   49 PHE cc_start: 0.8400 (t80) cc_final: 0.8129 (t80)
REVERT: C  135 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8434 (p)
REVERT: D   32 GLU cc_start: 0.8325 (tp30) cc_final: 0.8119 (tp30)
REVERT: E   24 GLN cc_start: 0.8872 (tm-30) cc_final: 0.7966 (tp40)
REVERT: E   72 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7703 (mm-30)
REVERT: G   24 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: G   32 GLU cc_start: 0.8484 (tp30) cc_final: 0.8212 (tp30)
REVERT: I   32 GLU cc_start: 0.8359 (tp30) cc_final: 0.7928 (tp30)
REVERT: I  135 SER cc_start: 0.8658 (p) cc_final: 0.8422 (p)
REVERT: K  103 SER cc_start: 0.8553 (t) cc_final: 0.8197 (p)
REVERT: F   32 GLU cc_start: 0.8326 (tp30) cc_final: 0.7901 (tp30)
REVERT: H  103 SER cc_start: 0.8683 (t) cc_final: 0.8339 (p)
REVERT: J   43 ASN cc_start: 0.8581 (t0) cc_final: 0.8379 (t0)
REVERT: J  120 ASP cc_start: 0.8047 (t0) cc_final: 0.7463 (t0)
REVERT: L   18 GLU cc_start: 0.7532 (mp0) cc_final: 0.7309 (tt0)
REVERT: L   24 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: L  148 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8205 (mm-30)
  outliers start: 53
  outliers final: 44
  residues processed: 324
  average time/residue: 0.1033
  time to fit residues: 51.7368
Evaluate side-chains
  309 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 263
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   74 MET
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   74 MET
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 103 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 152 optimal weight:    0.9990
   chunk 137 optimal weight:    8.9990
   chunk 124 optimal weight:    0.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  43 ASN
L  39 GLN
** L  55 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 = 0.3385 r_free = 0.3385 target = 0.093658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.081714 restraints weight = 31297.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.084781 restraints weight = 15778.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.086750 restraints weight = 9493.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.088192 restraints weight = 6491.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.089389 restraints weight = 4623.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13829  Z= 0.118
  Angle     :  0.496   9.537  18826  Z= 0.262
  Chirality :  0.035   0.152   2242
  Planarity :  0.004   0.055   2503
  Dihedral  :  4.454  67.677   1883
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.73 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.51 (0.20), residues: 1727
  helix:  3.42 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  0.69 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  50 
 PHE   0.032   0.002   PHE E  49 
 TRP   0.007   0.001   TRP H  42 
 HIS   0.006   0.001   HIS K  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13829)
  covalent geometry    : angle       0.49582 (18826)
  hydrogen bonds       : bond        0.03980 ( 1185)
  hydrogen bonds       : angle       3.21286 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 290
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8866 (tp40) cc_final: 0.8593 (tp40)
REVERT: A  100 PHE cc_start: 0.7749 (m-80) cc_final: 0.7377 (m-80)
REVERT: A  121 THR cc_start: 0.8203 (m) cc_final: 0.7963 (p)
REVERT: B   24 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8027 (tp40)
REVERT: B   65 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8686 (mm-30)
REVERT: B  144 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8677 (tt)
REVERT: C   32 GLU cc_start: 0.7979 (tp30) cc_final: 0.7605 (tp30)
REVERT: C   49 PHE cc_start: 0.8409 (t80) cc_final: 0.8147 (t80)
REVERT: C  135 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8452 (p)
REVERT: E   24 GLN cc_start: 0.8853 (tm-30) cc_final: 0.7944 (tp40)
REVERT: E   72 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7691 (mm-30)
REVERT: G   24 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8473 (tm-30)
REVERT: I   32 GLU cc_start: 0.8327 (tp30) cc_final: 0.7926 (tp30)
REVERT: I  135 SER cc_start: 0.8629 (p) cc_final: 0.8411 (p)
REVERT: I  157 GLU cc_start: 0.8797 (tp30) cc_final: 0.8583 (tm-30)
REVERT: K  103 SER cc_start: 0.8544 (t) cc_final: 0.8175 (p)
REVERT: K  157 GLU cc_start: 0.8847 (tp30) cc_final: 0.8636 (tp30)
REVERT: F   32 GLU cc_start: 0.8317 (tp30) cc_final: 0.7909 (tp30)
REVERT: L   18 GLU cc_start: 0.7544 (mp0) cc_final: 0.7278 (tt0)
REVERT: L   24 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8240 (tm-30)
REVERT: L  148 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8207 (mm-30)
  outliers start: 58
  outliers final: 48
  residues processed: 325
  average time/residue: 0.1068
  time to fit residues: 53.3262
Evaluate side-chains
  314 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 264
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   74 MET
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   74 MET
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 146 optimal weight:   10.0000
   chunk 96 optimal weight:    0.8980
   chunk 136 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 155 optimal weight:    0.9980
   chunk 151 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 163 optimal weight:    1.9990
   chunk 166 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  43 ASN
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  36 GLN
** L  55 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 = 0.3400 r_free = 0.3400 target = 0.094570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.082588 restraints weight = 31191.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.085664 restraints weight = 15766.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.087599 restraints weight = 9503.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.089196 restraints weight = 6524.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.090302 restraints weight = 4610.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13829  Z= 0.117
  Angle     :  0.506   9.326  18826  Z= 0.266
  Chirality :  0.034   0.160   2242
  Planarity :  0.004   0.056   2503
  Dihedral  :  4.469  71.528   1883
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.56 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.41 (0.20), residues: 1727
  helix:  3.39 (0.13), residues: 1428
  sheet:  None (None), residues: 0
  loop :  0.33 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  50 
 PHE   0.018   0.001   PHE C  19 
 TRP   0.008   0.001   TRP H  42 
 HIS   0.005   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (13829)
  covalent geometry    : angle       0.50623 (18826)
  hydrogen bonds       : bond        0.03834 ( 1185)
  hydrogen bonds       : angle       3.19672 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 297
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8884 (tp40) cc_final: 0.8528 (tp40)
REVERT: A  100 PHE cc_start: 0.7718 (m-80) cc_final: 0.7373 (m-80)
REVERT: A  121 THR cc_start: 0.8172 (m) cc_final: 0.7916 (p)
REVERT: A  157 GLU cc_start: 0.8527 (tp30) cc_final: 0.8251 (tp30)
REVERT: B   24 GLN cc_start: 0.8689 (tm-30) cc_final: 0.7978 (tp40)
REVERT: B   32 GLU cc_start: 0.8787 (tp30) cc_final: 0.8585 (tp30)
REVERT: B  144 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8652 (tt)
REVERT: C   32 GLU cc_start: 0.7940 (tp30) cc_final: 0.7584 (tp30)
REVERT: C  135 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8465 (p)
REVERT: D   49 PHE cc_start: 0.8837 (t80) cc_final: 0.8510 (t80)
REVERT: E   24 GLN cc_start: 0.8845 (tm-30) cc_final: 0.7934 (tp40)
REVERT: E   72 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7753 (mm-30)
REVERT: G   24 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: I   32 GLU cc_start: 0.8305 (tp30) cc_final: 0.7912 (tp30)
REVERT: I  135 SER cc_start: 0.8592 (p) cc_final: 0.8371 (p)
REVERT: K   24 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8330 (tp40)
REVERT: K  103 SER cc_start: 0.8549 (t) cc_final: 0.8174 (p)
REVERT: K  157 GLU cc_start: 0.8847 (tp30) cc_final: 0.8609 (tp30)
REVERT: F   32 GLU cc_start: 0.8208 (tp30) cc_final: 0.7805 (tp30)
REVERT: J   18 GLU cc_start: 0.7765 (mp0) cc_final: 0.7551 (tt0)
REVERT: L   18 GLU cc_start: 0.7546 (mp0) cc_final: 0.7329 (tt0)
REVERT: L   24 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: L  148 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8214 (mm-30)
  outliers start: 58
  outliers final: 45
  residues processed: 333
  average time/residue: 0.1054
  time to fit residues: 54.0509
Evaluate side-chains
  318 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 271
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  122 ILE
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   74 MET
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   74 MET
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 155 optimal weight:    1.9990
   chunk 81 optimal weight:    0.4980
   chunk 139 optimal weight:    0.9980
   chunk 164 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 150 optimal weight:    0.5980
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  43 ASN
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  55 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 = 0.3394 r_free = 0.3394 target = 0.094204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.082227 restraints weight = 31291.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.085293 restraints weight = 15908.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.087222 restraints weight = 9639.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088797 restraints weight = 6630.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.089933 restraints weight = 4673.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13829  Z= 0.123
  Angle     :  0.524  11.179  18826  Z= 0.273
  Chirality :  0.035   0.168   2242
  Planarity :  0.004   0.057   2503
  Dihedral  :  4.527  76.507   1883
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.77 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.41 (0.20), residues: 1727
  helix:  3.38 (0.13), residues: 1428
  sheet:  None (None), residues: 0
  loop :  0.35 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 114 
 PHE   0.016   0.001   PHE C  19 
 TRP   0.007   0.001   TRP H 152 
 HIS   0.005   0.001   HIS D  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13829)
  covalent geometry    : angle       0.52411 (18826)
  hydrogen bonds       : bond        0.03887 ( 1185)
  hydrogen bonds       : angle       3.20705 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 280
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8860 (tp40) cc_final: 0.8534 (tp40)
REVERT: A  100 PHE cc_start: 0.7777 (m-80) cc_final: 0.7436 (m-80)
REVERT: A  157 GLU cc_start: 0.8566 (tp30) cc_final: 0.8118 (tp30)
REVERT: B   24 GLN cc_start: 0.8705 (tm-30) cc_final: 0.7974 (tp40)
REVERT: C   32 GLU cc_start: 0.7946 (tp30) cc_final: 0.7600 (tp30)
REVERT: C  135 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8498 (p)
REVERT: D   18 GLU cc_start: 0.7502 (pm20) cc_final: 0.7091 (tt0)
REVERT: D   49 PHE cc_start: 0.8894 (t80) cc_final: 0.8653 (t80)
REVERT: E   24 GLN cc_start: 0.8848 (tm-30) cc_final: 0.7925 (tp40)
REVERT: E   32 GLU cc_start: 0.8357 (tp30) cc_final: 0.8086 (tp30)
REVERT: E   72 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7745 (mm-30)
REVERT: E  129 VAL cc_start: 0.7914 (t) cc_final: 0.7667 (t)
REVERT: G   24 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8505 (tm-30)
REVERT: G   32 GLU cc_start: 0.8516 (tp30) cc_final: 0.8233 (tp30)
REVERT: I   32 GLU cc_start: 0.8366 (tp30) cc_final: 0.7953 (tp30)
REVERT: I  135 SER cc_start: 0.8617 (p) cc_final: 0.8385 (p)
REVERT: K   24 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8305 (tp40)
REVERT: K  103 SER cc_start: 0.8566 (t) cc_final: 0.8187 (p)
REVERT: K  157 GLU cc_start: 0.8843 (tp30) cc_final: 0.8641 (tp30)
REVERT: J   18 GLU cc_start: 0.7784 (mp0) cc_final: 0.7565 (tt0)
REVERT: L   24 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: L   32 GLU cc_start: 0.8501 (tp30) cc_final: 0.8211 (tp30)
REVERT: L   55 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8180 (tp-100)
REVERT: L  148 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8170 (mm-30)
  outliers start: 57
  outliers final: 46
  residues processed: 315
  average time/residue: 0.0963
  time to fit residues: 48.2785
Evaluate side-chains
  310 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 263
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  122 ILE
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   74 MET
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  120 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 148 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  43 ASN
K  48 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  55 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 = 0.3279 r_free = 0.3279 target = 0.089891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.077612 restraints weight = 31888.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.080712 restraints weight = 16231.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.082756 restraints weight = 9785.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.084314 restraints weight = 6678.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.085478 restraints weight = 4722.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13829  Z= 0.145
  Angle     :  0.547  10.523  18826  Z= 0.286
  Chirality :  0.036   0.172   2242
  Planarity :  0.004   0.059   2503
  Dihedral  :  4.692  83.427   1883
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.97 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.36 (0.20), residues: 1727
  helix:  3.35 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.33 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  50 
 PHE   0.034   0.002   PHE C  49 
 TRP   0.008   0.001   TRP I 152 
 HIS   0.006   0.001   HIS D  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (13829)
  covalent geometry    : angle       0.54734 (18826)
  hydrogen bonds       : bond        0.04252 ( 1185)
  hydrogen bonds       : angle       3.26915 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 266
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8857 (tp40) cc_final: 0.8491 (tp40)
REVERT: A  100 PHE cc_start: 0.7933 (m-80) cc_final: 0.7566 (m-80)
REVERT: A  157 GLU cc_start: 0.8743 (tp30) cc_final: 0.8463 (tp30)
REVERT: B   24 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7966 (tp40)
REVERT: C   32 GLU cc_start: 0.7966 (tp30) cc_final: 0.7758 (tp30)
REVERT: C  133 ASP cc_start: 0.7169 (t0) cc_final: 0.6809 (t0)
REVERT: D   18 GLU cc_start: 0.7707 (pm20) cc_final: 0.7315 (tt0)
REVERT: E   24 GLN cc_start: 0.8827 (tm-30) cc_final: 0.7896 (tp40)
REVERT: E   72 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7695 (mm-30)
REVERT: G   24 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: G   32 GLU cc_start: 0.8491 (tp30) cc_final: 0.8230 (tp30)
REVERT: I   32 GLU cc_start: 0.8415 (tp30) cc_final: 0.7927 (tp30)
REVERT: I  133 ASP cc_start: 0.7129 (t0) cc_final: 0.6809 (t0)
REVERT: K   24 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8286 (tp40)
REVERT: K  103 SER cc_start: 0.8659 (t) cc_final: 0.8285 (p)
REVERT: K  148 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8294 (mm-30)
REVERT: K  153 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8871 (tt)
REVERT: J   18 GLU cc_start: 0.7945 (mp0) cc_final: 0.7668 (tt0)
REVERT: J   32 GLU cc_start: 0.8452 (tp30) cc_final: 0.8115 (tp30)
REVERT: J  133 ASP cc_start: 0.6836 (t0) cc_final: 0.6578 (t0)
REVERT: L   24 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8147 (tm-30)
  outliers start: 62
  outliers final: 45
  residues processed: 309
  average time/residue: 0.0957
  time to fit residues: 47.0177
Evaluate side-chains
  302 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 256
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  122 ILE
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  120 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 81 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 160 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 148 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 GLN
K  48 ASN
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  55 GLN
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 158 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.094460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.082320 restraints weight = 30930.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.085450 restraints weight = 15626.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.087592 restraints weight = 9465.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.089088 restraints weight = 6322.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090244 restraints weight = 4505.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13829  Z= 0.122
  Angle     :  0.535  10.544  18826  Z= 0.278
  Chirality :  0.034   0.197   2242
  Planarity :  0.004   0.056   2503
  Dihedral  :  4.738  89.168   1883
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.59 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.38 (0.20), residues: 1727
  helix:  3.35 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.39 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 124 
 PHE   0.016   0.001   PHE I  49 
 TRP   0.009   0.001   TRP B 152 
 HIS   0.006   0.001   HIS J  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (13829)
  covalent geometry    : angle       0.53504 (18826)
  hydrogen bonds       : bond        0.03876 ( 1185)
  hydrogen bonds       : angle       3.20858 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 288
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 GLU cc_start: 0.8391 (tp30) cc_final: 0.7492 (tp30)
REVERT: A   36 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.6664 (mp10)
REVERT: A   55 GLN cc_start: 0.8829 (tp40) cc_final: 0.8460 (tp40)
REVERT: A   74 MET cc_start: 0.9052 (ttp) cc_final: 0.8829 (ptt)
REVERT: A  100 PHE cc_start: 0.7875 (m-80) cc_final: 0.7533 (m-80)
REVERT: A  157 GLU cc_start: 0.8673 (tp30) cc_final: 0.8333 (tp30)
REVERT: B   24 GLN cc_start: 0.8708 (tm-30) cc_final: 0.7996 (tp40)
REVERT: D   18 GLU cc_start: 0.7509 (pm20) cc_final: 0.7142 (tt0)
REVERT: D   32 GLU cc_start: 0.8430 (tp30) cc_final: 0.8201 (tp30)
REVERT: E   24 GLN cc_start: 0.8819 (tm-30) cc_final: 0.7827 (tp40)
REVERT: E   32 GLU cc_start: 0.8313 (tp30) cc_final: 0.8057 (tp30)
REVERT: E   72 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7763 (mm-30)
REVERT: G   24 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8482 (tm-30)
REVERT: G   32 GLU cc_start: 0.8413 (tp30) cc_final: 0.8145 (tp30)
REVERT: I   32 GLU cc_start: 0.8359 (tp30) cc_final: 0.7953 (tp30)
REVERT: K   24 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8275 (tp40)
REVERT: K  103 SER cc_start: 0.8684 (t) cc_final: 0.8312 (p)
REVERT: F   32 GLU cc_start: 0.8484 (tp30) cc_final: 0.7897 (tp30)
REVERT: H   96 GLU cc_start: 0.8481 (pm20) cc_final: 0.8126 (pm20)
REVERT: J   18 GLU cc_start: 0.7800 (mp0) cc_final: 0.7546 (tt0)
REVERT: J   32 GLU cc_start: 0.8431 (tp30) cc_final: 0.8079 (tp30)
REVERT: L   24 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: L  148 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8254 (mm-30)
  outliers start: 42
  outliers final: 40
  residues processed: 316
  average time/residue: 0.1037
  time to fit residues: 50.5903
Evaluate side-chains
  307 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 266
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  120 ASP
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   52 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   74 MET
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  120 ASP
Chi-restraints excluded: chain J residue  144 ILE
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 157 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 147 optimal weight:    7.9990
   chunk 119 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 154 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  24 GLN
K  48 ASN
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 150 GLN
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  36 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.085783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.073781 restraints weight = 32341.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.076714 restraints weight = 16552.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.078634 restraints weight = 10176.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.080027 restraints weight = 7063.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.081211 restraints weight = 5148.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  13829  Z= 0.232
  Angle     :  0.665  10.755  18826  Z= 0.347
  Chirality :  0.039   0.185   2242
  Planarity :  0.005   0.065   2503
  Dihedral  :  5.080  87.703   1883
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.39 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.89 (0.20), residues: 1727
  helix:  3.03 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.14 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 124 
 PHE   0.038   0.002   PHE I  49 
 TRP   0.014   0.002   TRP K  42 
 HIS   0.006   0.001   HIS K  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (13829)
  covalent geometry    : angle       0.66529 (18826)
  hydrogen bonds       : bond        0.05267 ( 1185)
  hydrogen bonds       : angle       3.60201 ( 3555)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 247
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8952 (tp40) cc_final: 0.8616 (tp40)
REVERT: A   74 MET cc_start: 0.9160 (ttp) cc_final: 0.8924 (ptt)
REVERT: A  100 PHE cc_start: 0.8076 (m-80) cc_final: 0.7856 (m-80)
REVERT: A  132 GLU cc_start: 0.7905 (tp30) cc_final: 0.7207 (tp30)
REVERT: A  133 ASP cc_start: 0.7391 (t0) cc_final: 0.7115 (t0)
REVERT: C   32 GLU cc_start: 0.8542 (tp30) cc_final: 0.8170 (tp30)
REVERT: D   18 GLU cc_start: 0.7656 (pm20) cc_final: 0.7368 (tt0)
REVERT: E   32 GLU cc_start: 0.8481 (tp30) cc_final: 0.8265 (tp30)
REVERT: E   72 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8047 (mm-30)
REVERT: I  133 ASP cc_start: 0.7348 (t0) cc_final: 0.7141 (t0)
REVERT: K   18 GLU cc_start: 0.7928 (mp0) cc_final: 0.7706 (tt0)
REVERT: K  103 SER cc_start: 0.8785 (t) cc_final: 0.8422 (p)
REVERT: K  148 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: H   96 GLU cc_start: 0.8582 (pm20) cc_final: 0.8320 (pm20)
REVERT: H  103 SER cc_start: 0.8835 (t) cc_final: 0.8542 (p)
REVERT: J  133 ASP cc_start: 0.7068 (t0) cc_final: 0.6836 (t0)
  outliers start: 48
  outliers final: 41
  residues processed: 280
  average time/residue: 0.0961
  time to fit residues: 42.8679
Evaluate side-chains
  279 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 238
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  122 ILE
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   74 MET
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  144 ILE
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 164 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 135 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 134 optimal weight:    7.9990
   chunk 158 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  48 ASN
K  48 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  55 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.090390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.078638 restraints weight = 31612.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.081639 restraints weight = 15928.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.083672 restraints weight = 9649.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085157 restraints weight = 6493.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.086256 restraints weight = 4648.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13829  Z= 0.141
  Angle     :  0.581  11.302  18826  Z= 0.303
  Chirality :  0.035   0.189   2242
  Planarity :  0.004   0.059   2503
  Dihedral  :  4.950  87.055   1883
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.40 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.12 (0.20), residues: 1727
  helix:  3.18 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.26 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 124 
 PHE   0.019   0.001   PHE I  49 
 TRP   0.013   0.001   TRP I 152 
 HIS   0.006   0.002   HIS J  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (13829)
  covalent geometry    : angle       0.58145 (18826)
  hydrogen bonds       : bond        0.04473 ( 1185)
  hydrogen bonds       : angle       3.34395 ( 3555)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1984.92 seconds
wall clock time: 35 minutes 24.67 seconds (2124.67 seconds total)