Starting phenix.real_space_refine
on Sun Apr  5 02:01:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mb8_63769/04_2026/9mb8_63769.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mb8_63769/04_2026/9mb8_63769.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mb8_63769/04_2026/9mb8_63769.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mb8_63769/04_2026/9mb8_63769.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mb8_63769/04_2026/9mb8_63769.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mb8_63769/04_2026/9mb8_63769.map"
  }
  resolution = 3.67
  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=  -0.015 sd=   0.452
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      32      5.16       5
     C    4532      2.51       5
     N    1264      2.21       5
     O    1284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7112
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2079
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
    Chain: "C"
      Number of atoms: 1487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1487
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 9, 'TRANS': 168}
    Chain: "A"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2079
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
    Chain: "D"
      Number of atoms: 1467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1467
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 9, 'TRANS': 166}
  Time building chain proxies: 1.33, per 1000 atoms: 0.19
  Number of scatterers: 7112
  At special positions: 0
  Unit cell: (124.64, 110.7, 59.86, 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      32     16.00
     O    1284      8.00
     N    1264      7.00
     C    4532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 109 " - pdb=" SG  CYS C 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 109 " - pdb=" SG  CYS D 112 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 264.7 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 8 sheets defined
      50.1% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 81 through 86
      removed outlier: 3.981A  pdb=" N   TRP B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   SER B  86 " --> pdb=" O   GLN B  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 86'
    Processing helix  chain 'B' and resid 87 through 92
      removed outlier: 4.227A  pdb=" N   TYR B  91 " --> pdb=" O   ARG B  87 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 87 through 92'
    Processing helix  chain 'B' and resid 110 through 114
    Processing helix  chain 'B' and resid 121 through 136
      removed outlier: 3.942A  pdb=" N   TYR B 125 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 136 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 159
      removed outlier: 3.540A  pdb=" N   ALA B 156 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 157 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 187 through 201
    Processing helix  chain 'B' and resid 201 through 215
      removed outlier: 3.682A  pdb=" N   TRP B 205 " --> pdb=" O   ASN B 201 " (cutoff:3.500A)
      Proline residue:  B 211  - end of helix
    Processing helix  chain 'B' and resid 218 through 231
      removed outlier: 3.657A  pdb=" N   VAL B 222 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 245
    Processing helix  chain 'B' and resid 246 through 248
      No H-bonds generated for 'chain 'B' and resid 246 through 248'
    Processing helix  chain 'B' and resid 249 through 254
      removed outlier: 3.780A  pdb=" N   LEU B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   GLY B 254 " --> pdb=" O   ARG B 250 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 254'
    Processing helix  chain 'B' and resid 273 through 282
      removed outlier: 3.598A  pdb=" N   ALA B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.617A  pdb=" N   ALA B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 315
    Processing helix  chain 'C' and resid 35 through 39
      removed outlier: 3.508A  pdb=" N   GLU C  39 " --> pdb=" O   ARG C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 58
      removed outlier: 3.752A  pdb=" N   ALA C  58 " --> pdb=" O   ARG C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 81
    Processing helix  chain 'C' and resid 83 through 103
      removed outlier: 3.841A  pdb=" N   GLU C  88 " --> pdb=" O   ARG C  84 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU C  89 " --> pdb=" O   ILE C  85 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LYS C  91 " --> pdb=" O   ASN C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 115
      removed outlier: 3.680A  pdb=" N   GLU C 113 " --> pdb=" O   CYS C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 120
    Processing helix  chain 'A' and resid 54 through 61
      removed outlier: 3.683A  pdb=" N   GLN A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
      removed outlier: 3.878A  pdb=" N   TRP A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A  86 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 81 through 86'
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 4.144A  pdb=" N   TYR A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A  92 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 92'
    Processing helix  chain 'A' and resid 110 through 114
    Processing helix  chain 'A' and resid 121 through 136
      removed outlier: 3.953A  pdb=" N   TYR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 136 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 159
    Processing helix  chain 'A' and resid 187 through 201
    Processing helix  chain 'A' and resid 202 through 215
      Proline residue:  A 211  - end of helix
    Processing helix  chain 'A' and resid 218 through 231
      removed outlier: 3.618A  pdb=" N   VAL A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 246
    Processing helix  chain 'A' and resid 249 through 256
      removed outlier: 3.695A  pdb=" N   VAL A 252 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 253 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLY A 254 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 256 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 282
      removed outlier: 3.679A  pdb=" N   ALA A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.676A  pdb=" N   ALA A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 315
    Processing helix  chain 'D' and resid 33 through 38
      removed outlier: 4.051A  pdb=" N   PHE D  37 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 45
      No H-bonds generated for 'chain 'D' and resid 43 through 45'
    Processing helix  chain 'D' and resid 46 through 58
      removed outlier: 3.592A  pdb=" N   LEU D  50 " --> pdb=" O   ARG D  46 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ALA D  58 " --> pdb=" O   ARG D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 81
      removed outlier: 3.549A  pdb=" N   LYS D  81 " --> pdb=" O   MET D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 103
      removed outlier: 3.925A  pdb=" N   GLU D  88 " --> pdb=" O   ARG D  84 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LYS D  91 " --> pdb=" O   ASN D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 115
      removed outlier: 3.683A  pdb=" N   GLU D 113 " --> pdb=" O   CYS D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 121
    Processing sheet with id=AA1, first strand: chain 'B' and resid 164 through 167
      removed outlier: 8.097A  pdb=" N   CYS B 141 " --> pdb=" O   ALA B 165 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B 167 " --> pdb=" O   CYS B 141 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   PHE B 143 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B  71 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   VAL B 144 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL B  73 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL B  72 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   GLY B  66 " --> pdb=" O   TYR C 130 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   TYR C 130 " --> pdb=" O   GLY B  66 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 260 through 265
      removed outlier: 6.615A  pdb=" N   CYS B 260 " --> pdb=" O   THR B 288 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   GLU B 290 " --> pdb=" O   CYS B 260 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   VAL B 262 " --> pdb=" O   GLU B 290 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU B 292 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   GLN B 264 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 136
    Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 171
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 167
      removed outlier: 8.184A  pdb=" N   CYS A 141 " --> pdb=" O   ALA A 165 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU A 167 " --> pdb=" O   CYS A 141 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   PHE A 143 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL A  71 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   VAL A 144 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   VAL A  73 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL A  72 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   GLY A  66 " --> pdb=" O   TYR D 130 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TYR D 130 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 265
      removed outlier: 6.714A  pdb=" N   CYS A 260 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   GLU A 290 " --> pdb=" O   CYS A 260 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL A 262 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU A 292 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 135 through 136
    Processing sheet with id=AA8, first strand: chain 'D' and resid 169 through 171

    256 hydrogen bonds defined for protein.
    732 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: 0.86

  Time building geometry restraints manager: 0.90 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: 2361
        1.34 -     1.46: 1490
        1.46 -     1.58: 3374
        1.58 -     1.69: 1
        1.69 -     1.81: 50
  Bond restraints: 7276
  Sorted by residual:
  bond pdb=" CA  LEU D  31 "
       pdb=" CB  LEU D  31 "
    ideal  model  delta    sigma   weight residual
    1.526  1.569 -0.043 1.51e-02 4.39e+03 8.14e+00
  bond pdb=" CB  PRO B  50 "
       pdb=" CG  PRO B  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.604 -0.112 5.00e-02 4.00e+02 5.04e+00
  bond pdb=" CG  PRO B  50 "
       pdb=" CD  PRO B  50 "
    ideal  model  delta    sigma   weight residual
    1.503  1.436  0.067 3.40e-02 8.65e+02 3.83e+00
  bond pdb=" CA  PRO A 272 "
       pdb=" CB  PRO A 272 "
    ideal  model  delta    sigma   weight residual
    1.533  1.516  0.017 1.34e-02 5.57e+03 1.62e+00
  bond pdb=" CB  PRO B 272 "
       pdb=" CG  PRO B 272 "
    ideal  model  delta    sigma   weight residual
    1.492  1.551 -0.059 5.00e-02 4.00e+02 1.41e+00
  ... (remaining 7271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 9645
        2.23 -     4.46: 204
        4.46 -     6.70: 28
        6.70 -     8.93: 8
        8.93 -    11.16: 5
  Bond angle restraints: 9890
  Sorted by residual:
  angle pdb=" C   VAL A 271 "
        pdb=" N   PRO A 272 "
        pdb=" CA  PRO A 272 "
      ideal   model   delta    sigma   weight residual
     119.76  127.07   -7.31 1.00e+00 1.00e+00 5.34e+01
  angle pdb=" CA  PRO B  50 "
        pdb=" N   PRO B  50 "
        pdb=" CD  PRO B  50 "
      ideal   model   delta    sigma   weight residual
     112.00  102.88    9.12 1.40e+00 5.10e-01 4.24e+01
  angle pdb=" C   SER A 147 "
        pdb=" CA  SER A 147 "
        pdb=" CB  SER A 147 "
      ideal   model   delta    sigma   weight residual
     117.23  110.46    6.77 1.36e+00 5.41e-01 2.47e+01
  angle pdb=" C   SER B 147 "
        pdb=" CA  SER B 147 "
        pdb=" CB  SER B 147 "
      ideal   model   delta    sigma   weight residual
     117.23  110.47    6.76 1.36e+00 5.41e-01 2.47e+01
  angle pdb=" N   PRO B  50 "
        pdb=" CD  PRO B  50 "
        pdb=" CG  PRO B  50 "
      ideal   model   delta    sigma   weight residual
     103.20   96.53    6.67 1.50e+00 4.44e-01 1.98e+01
  ... (remaining 9885 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 3586
       16.06 -    32.11: 560
       32.11 -    48.17: 163
       48.17 -    64.22: 49
       64.22 -    80.28: 6
  Dihedral angle restraints: 4364
    sinusoidal: 1746
      harmonic: 2618
  Sorted by residual:
  dihedral pdb=" CB  CYS D 109 "
           pdb=" SG  CYS D 109 "
           pdb=" SG  CYS D 112 "
           pdb=" CB  CYS D 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.28   80.28     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CB  CYS C 109 "
           pdb=" SG  CYS C 109 "
           pdb=" SG  CYS C 112 "
           pdb=" CB  CYS C 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.32   79.32     1      1.00e+01 1.00e-02 7.82e+01
  dihedral pdb=" CA  ALA D  22 "
           pdb=" C   ALA D  22 "
           pdb=" N   ASP D  23 "
           pdb=" CA  ASP D  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.51  -28.49     0      5.00e+00 4.00e-02 3.25e+01
  ... (remaining 4361 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 915
       0.062 -    0.123: 186
       0.123 -    0.185: 10
       0.185 -    0.246: 1
       0.246 -    0.308: 2
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CB  THR D 107 "
            pdb=" CA  THR D 107 "
            pdb=" OG1 THR D 107 "
            pdb=" CG2 THR D 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CG  LEU D  38 "
            pdb=" CB  LEU D  38 "
            pdb=" CD1 LEU D  38 "
            pdb=" CD2 LEU D  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CB  THR C 107 "
            pdb=" CA  THR C 107 "
            pdb=" OG1 THR C 107 "
            pdb=" CG2 THR C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1111 not shown)

  Planarity restraints: 1276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  49 "    0.078 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO B  50 "   -0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO B  50 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO B  50 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 271 "    0.061 5.00e-02 4.00e+02   9.09e-02 1.32e+01
        pdb=" N   PRO B 272 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO B 272 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 272 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 258 "   -0.058 5.00e-02 4.00e+02   8.75e-02 1.23e+01
        pdb=" N   PRO B 259 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "   -0.048 5.00e-02 4.00e+02
  ... (remaining 1273 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 215
        2.70 -     3.25: 7348
        3.25 -     3.80: 11276
        3.80 -     4.35: 13904
        4.35 -     4.90: 22841
  Nonbonded interactions: 55584
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  21 "
            pdb=" NH1 ARG D  46 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" OD1 ASN C  51 "
            pdb=" NH2 ARG C  54 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" O   ILE D  61 "
            pdb=" OH  TYR D 104 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" O   HIS A 146 "
            pdb=" OG  SER A 149 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG  SER A  86 "
            pdb=" N   ARG A  87 "
     model   vdw
     2.206 3.120
  ... (remaining 55579 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 20 through 195)
  selection = chain 'D'
}

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:             1.800
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.160
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   7278  Z= 0.161
  Angle     :  0.789  11.158   9894  Z= 0.411
  Chirality :  0.048   0.308   1114
  Planarity :  0.008   0.112   1276
  Dihedral  : 17.379  76.812   2670
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.27 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 36.05 %
    Favored  : 63.18 %
  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 are not related in a simple way.
  whole: -1.01 (0.28), residues: 886
  helix:  0.71 (0.28), residues: 328
  sheet:  0.42 (0.50), residues: 90
  loop : -2.01 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C  36 
 TYR   0.021   0.001   TYR D 130 
 PHE   0.018   0.001   PHE A 164 
 TRP   0.006   0.001   TRP B  85 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 7276)
  covalent geometry    : angle       0.78935 ( 9890)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.27920 (    4)
  hydrogen bonds       : bond        0.18748 (  256)
  hydrogen bonds       : angle       6.13332 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 247
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 251
  average time/residue: 0.1140
  time to fit residues: 35.4512
Evaluate side-chains
  243 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 239
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  157 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 146 HIS
A 146 HIS
** D 157 HIS ** 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 = 0.3106 r_free = 0.3106 target = 0.071787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.064358 restraints weight = 19537.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.066317 restraints weight = 9184.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.067585 restraints weight = 5186.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.068413 restraints weight = 3284.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.068963 restraints weight = 2273.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7278  Z= 0.159
  Angle     :  0.689   9.375   9894  Z= 0.343
  Chirality :  0.047   0.210   1114
  Planarity :  0.006   0.063   1276
  Dihedral  :  5.993  59.977   1006
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.48 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 31.27 %
    Favored  : 63.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.28), residues: 886
  helix:  0.86 (0.28), residues: 340
  sheet:  0.61 (0.52), residues: 90
  loop : -2.05 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  36 
 TYR   0.009   0.001   TYR D  78 
 PHE   0.018   0.001   PHE B 245 
 TRP   0.006   0.001   TRP D  97 
 HIS   0.007   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7276)
  covalent geometry    : angle       0.68911 ( 9890)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.18230 (    4)
  hydrogen bonds       : bond        0.04289 (  256)
  hydrogen bonds       : angle       4.28959 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 244
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5741 (pmt-80)
REVERT: C  131 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7755 (tt0)
REVERT: A   94 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.5998 (pmt-80)
REVERT: D   56 MET cc_start: 0.7687 (tpp) cc_final: 0.7354 (tpp)
REVERT: D   75 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7456 (t0)
REVERT: D  126 SER cc_start: 0.8604 (t) cc_final: 0.8197 (m)
REVERT: D  178 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8454 (mtpp)
  outliers start: 41
  outliers final: 20
  residues processed: 267
  average time/residue: 0.1129
  time to fit residues: 37.4482
Evaluate side-chains
  264 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 239
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0050
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 GLN
A 146 HIS
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.069346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.062316 restraints weight = 19263.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.064140 restraints weight = 9118.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.065338 restraints weight = 5224.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.066132 restraints weight = 3330.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.066678 restraints weight = 2323.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7278  Z= 0.191
  Angle     :  0.707   9.203   9894  Z= 0.353
  Chirality :  0.048   0.225   1114
  Planarity :  0.006   0.063   1276
  Dihedral  :  5.763  59.416   1002
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.71 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 31.52 %
    Favored  : 61.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.29), residues: 886
  helix:  0.94 (0.28), residues: 340
  sheet:  0.63 (0.55), residues: 90
  loop : -2.11 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 286 
 TYR   0.012   0.001   TYR D  78 
 PHE   0.018   0.001   PHE B 143 
 TRP   0.007   0.001   TRP A 205 
 HIS   0.012   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7276)
  covalent geometry    : angle       0.70688 ( 9890)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       0.17174 (    4)
  hydrogen bonds       : bond        0.04359 (  256)
  hydrogen bonds       : angle       4.06820 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 247
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5636 (pmt-80)
REVERT: B  151 MET cc_start: 0.8042 (tpp) cc_final: 0.7804 (ttp)
REVERT: C   56 MET cc_start: 0.7204 (tpp) cc_final: 0.6940 (tpp)
REVERT: A   94 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6283 (pmt-80)
REVERT: A  232 MET cc_start: 0.7744 (ptt) cc_final: 0.7508 (ptt)
REVERT: D   36 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7800 (mmm160)
REVERT: D   40 TYR cc_start: 0.8021 (m-80) cc_final: 0.7746 (m-80)
REVERT: D   75 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7521 (t0)
REVERT: D  126 SER cc_start: 0.8632 (t) cc_final: 0.8327 (m)
REVERT: D  142 TYR cc_start: 0.8233 (m-80) cc_final: 0.7873 (m-80)
REVERT: D  178 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8490 (mtpp)
  outliers start: 51
  outliers final: 33
  residues processed: 281
  average time/residue: 0.1113
  time to fit residues: 39.1083
Evaluate side-chains
  271 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 234
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   55 HIS
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  157 HIS
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 86 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 GLN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 157 HIS ** 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 = 0.3147 r_free = 0.3147 target = 0.074121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.066885 restraints weight = 19201.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.068801 restraints weight = 9143.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.070022 restraints weight = 5160.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.070827 restraints weight = 3264.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.071363 restraints weight = 2258.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7278  Z= 0.149
  Angle     :  0.686   9.266   9894  Z= 0.340
  Chirality :  0.047   0.236   1114
  Planarity :  0.006   0.062   1276
  Dihedral  :  5.636  59.504   1002
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.59 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 29.59 %
    Favored  : 63.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.28), residues: 886
  helix:  0.80 (0.28), residues: 343
  sheet:  0.67 (0.56), residues: 90
  loop : -2.10 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  36 
 TYR   0.012   0.001   TYR D  78 
 PHE   0.019   0.001   PHE B 143 
 TRP   0.007   0.001   TRP A 205 
 HIS   0.005   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7276)
  covalent geometry    : angle       0.68573 ( 9890)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       0.18431 (    4)
  hydrogen bonds       : bond        0.03864 (  256)
  hydrogen bonds       : angle       3.91254 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 242
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5580 (pmt-80)
REVERT: B  170 ILE cc_start: 0.8460 (mt) cc_final: 0.8176 (tt)
REVERT: C   56 MET cc_start: 0.7067 (tpp) cc_final: 0.6805 (tpp)
REVERT: C   71 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8329 (mmmm)
REVERT: C  126 SER cc_start: 0.8615 (t) cc_final: 0.8281 (m)
REVERT: C  131 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7714 (tt0)
REVERT: A   94 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.5935 (pmt-80)
REVERT: A  232 MET cc_start: 0.7881 (ptt) cc_final: 0.7590 (ptt)
REVERT: A  242 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8132 (mm-40)
REVERT: A  268 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7289 (m-30)
REVERT: D   75 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7379 (t0)
REVERT: D  126 SER cc_start: 0.8607 (t) cc_final: 0.8261 (m)
REVERT: D  142 TYR cc_start: 0.8183 (m-80) cc_final: 0.7855 (m-80)
REVERT: D  178 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8480 (mtpp)
  outliers start: 55
  outliers final: 40
  residues processed: 280
  average time/residue: 0.1099
  time to fit residues: 38.5055
Evaluate side-chains
  287 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 240
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   55 HIS
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 GLN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 157 HIS ** 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 = 0.3009 r_free = 0.3009 target = 0.067036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.060067 restraints weight = 19492.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.061922 restraints weight = 9153.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.063106 restraints weight = 5141.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.063890 restraints weight = 3243.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.064427 restraints weight = 2244.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   7278  Z= 0.247
  Angle     :  0.780   9.194   9894  Z= 0.391
  Chirality :  0.051   0.277   1114
  Planarity :  0.006   0.064   1276
  Dihedral  :  6.007  59.096   1002
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.05 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  8.40 %
    Allowed  : 29.33 %
    Favored  : 62.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 886
  helix:  0.68 (0.28), residues: 349
  sheet:  0.51 (0.56), residues: 90
  loop : -2.16 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  36 
 TYR   0.012   0.001   TYR D  78 
 PHE   0.019   0.002   PHE B 143 
 TRP   0.008   0.001   TRP A 205 
 HIS   0.006   0.002   HIS B 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 7276)
  covalent geometry    : angle       0.78050 ( 9890)
  SS BOND              : bond        0.00057 (    2)
  SS BOND              : angle       0.13993 (    4)
  hydrogen bonds       : bond        0.04855 (  256)
  hydrogen bonds       : angle       4.16250 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 255
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  121 ASN cc_start: 0.8341 (t0) cc_final: 0.8114 (t0)
REVERT: B  151 MET cc_start: 0.8059 (tpp) cc_final: 0.7722 (ttm)
REVERT: B  291 PHE cc_start: 0.8048 (t80) cc_final: 0.7837 (t80)
REVERT: C   56 MET cc_start: 0.7229 (tpp) cc_final: 0.6911 (tpp)
REVERT: C   69 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6154 (t80)
REVERT: C  126 SER cc_start: 0.8760 (t) cc_final: 0.8462 (m)
REVERT: C  131 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7902 (tt0)
REVERT: C  178 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8455 (mtpp)
REVERT: A  179 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.6053 (t0)
REVERT: A  232 MET cc_start: 0.8143 (ptt) cc_final: 0.7692 (ptt)
REVERT: A  282 HIS cc_start: 0.8271 (m170) cc_final: 0.8050 (m170)
REVERT: D   75 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7631 (t0)
REVERT: D  126 SER cc_start: 0.8716 (t) cc_final: 0.8328 (m)
REVERT: D  127 ASN cc_start: 0.8707 (p0) cc_final: 0.8308 (p0)
REVERT: D  178 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8511 (mtpp)
  outliers start: 65
  outliers final: 45
  residues processed: 297
  average time/residue: 0.1050
  time to fit residues: 39.4365
Evaluate side-chains
  294 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 243
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  179 ASP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   55 HIS
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  157 HIS
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 GLN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.073164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.065971 restraints weight = 19319.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.067854 restraints weight = 9197.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.069055 restraints weight = 5213.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.069862 restraints weight = 3313.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.070314 restraints weight = 2298.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7278  Z= 0.155
  Angle     :  0.709   9.661   9894  Z= 0.353
  Chirality :  0.048   0.261   1114
  Planarity :  0.006   0.064   1276
  Dihedral  :  5.754  59.535   1002
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.92 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 29.33 %
    Favored  : 63.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.28), residues: 886
  helix:  0.75 (0.28), residues: 341
  sheet:  0.50 (0.71), residues: 62
  loop : -1.96 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 117 
 TYR   0.013   0.001   TYR D  78 
 PHE   0.022   0.001   PHE B 143 
 TRP   0.008   0.001   TRP A 205 
 HIS   0.005   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 7276)
  covalent geometry    : angle       0.70914 ( 9890)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.13036 (    4)
  hydrogen bonds       : bond        0.03876 (  256)
  hydrogen bonds       : angle       3.91329 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 251
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.5677 (pmt-80)
REVERT: B  121 ASN cc_start: 0.8352 (t0) cc_final: 0.8109 (t0)
REVERT: B  151 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7672 (ttm)
REVERT: B  198 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8102 (ppp)
REVERT: B  268 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7033 (m-30)
REVERT: C   41 ILE cc_start: 0.9178 (tp) cc_final: 0.8915 (tt)
REVERT: C   56 MET cc_start: 0.7148 (tpp) cc_final: 0.6845 (tpp)
REVERT: C   71 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8295 (mmmm)
REVERT: C   79 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7881 (tm-30)
REVERT: C   88 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8198 (mm-30)
REVERT: C  126 SER cc_start: 0.8681 (t) cc_final: 0.8328 (m)
REVERT: C  131 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7736 (tt0)
REVERT: C  178 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8358 (mtpp)
REVERT: A   94 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.5948 (pmt-80)
REVERT: A  232 MET cc_start: 0.8079 (ptt) cc_final: 0.7706 (ptt)
REVERT: A  268 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7376 (m-30)
REVERT: D   75 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7544 (t0)
REVERT: D  126 SER cc_start: 0.8655 (t) cc_final: 0.8240 (m)
REVERT: D  127 ASN cc_start: 0.8663 (p0) cc_final: 0.8237 (p0)
REVERT: D  178 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8475 (mtpp)
  outliers start: 59
  outliers final: 37
  residues processed: 288
  average time/residue: 0.1089
  time to fit residues: 39.1667
Evaluate side-chains
  295 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 248
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ASP
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 GLN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 HIS
** D 157 HIS ** 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 = 0.3039 r_free = 0.3039 target = 0.068503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.061608 restraints weight = 19372.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.063446 restraints weight = 9163.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.064631 restraints weight = 5147.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.065400 restraints weight = 3247.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.065886 restraints weight = 2244.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7278  Z= 0.183
  Angle     :  0.745   9.801   9894  Z= 0.372
  Chirality :  0.050   0.315   1114
  Planarity :  0.006   0.064   1276
  Dihedral  :  5.770  59.390   1002
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.59 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  7.88 %
    Allowed  : 31.01 %
    Favored  : 61.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.28), residues: 886
  helix:  0.64 (0.28), residues: 349
  sheet:  0.39 (0.71), residues: 62
  loop : -2.00 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 117 
 TYR   0.012   0.001   TYR C  78 
 PHE   0.023   0.001   PHE B 143 
 TRP   0.008   0.001   TRP A 205 
 HIS   0.005   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 7276)
  covalent geometry    : angle       0.74562 ( 9890)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       0.12248 (    4)
  hydrogen bonds       : bond        0.04135 (  256)
  hydrogen bonds       : angle       3.95039 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 253
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.5738 (pmt-80)
REVERT: B  117 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7876 (ttm110)
REVERT: B  121 ASN cc_start: 0.8331 (t0) cc_final: 0.8076 (t0)
REVERT: B  151 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7709 (ttm)
REVERT: B  232 MET cc_start: 0.7376 (ptt) cc_final: 0.7170 (ptt)
REVERT: C   41 ILE cc_start: 0.9184 (tp) cc_final: 0.8942 (tt)
REVERT: C   56 MET cc_start: 0.7191 (tpp) cc_final: 0.6791 (tpp)
REVERT: C   79 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: C  116 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8543 (ttmm)
REVERT: C  126 SER cc_start: 0.8699 (t) cc_final: 0.8365 (m)
REVERT: C  131 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7815 (tt0)
REVERT: C  178 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8324 (mtpp)
REVERT: A   94 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6078 (pmt-80)
REVERT: A  232 MET cc_start: 0.8197 (ptt) cc_final: 0.7814 (ptt)
REVERT: D   75 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7570 (t0)
REVERT: D   77 MET cc_start: 0.7947 (mtt) cc_final: 0.7655 (mtt)
REVERT: D  126 SER cc_start: 0.8691 (t) cc_final: 0.8279 (m)
REVERT: D  127 ASN cc_start: 0.8679 (p0) cc_final: 0.8252 (p0)
REVERT: D  178 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8520 (mtpp)
  outliers start: 61
  outliers final: 44
  residues processed: 293
  average time/residue: 0.1059
  time to fit residues: 38.9819
Evaluate side-chains
  297 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 246
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 HIS
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.068709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.061818 restraints weight = 19533.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.063642 restraints weight = 9111.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.064832 restraints weight = 5132.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.065619 restraints weight = 3242.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.066148 restraints weight = 2238.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7278  Z= 0.181
  Angle     :  0.761  10.343   9894  Z= 0.378
  Chirality :  0.049   0.289   1114
  Planarity :  0.006   0.064   1276
  Dihedral  :  5.754  59.518   1002
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  9.71 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  7.88 %
    Allowed  : 31.27 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.28), residues: 886
  helix:  0.58 (0.28), residues: 347
  sheet:  0.39 (0.71), residues: 62
  loop : -1.94 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 117 
 TYR   0.016   0.001   TYR D  78 
 PHE   0.020   0.001   PHE B 143 
 TRP   0.008   0.001   TRP A 205 
 HIS   0.010   0.002   HIS A 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7276)
  covalent geometry    : angle       0.76143 ( 9890)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.15020 (    4)
  hydrogen bonds       : bond        0.04108 (  256)
  hydrogen bonds       : angle       3.98276 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 241
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5743 (pmt-80)
REVERT: B  151 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7732 (ttm)
REVERT: B  232 MET cc_start: 0.7387 (ptt) cc_final: 0.7169 (ptt)
REVERT: B  282 HIS cc_start: 0.8404 (m170) cc_final: 0.8186 (m170)
REVERT: C   79 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: C   88 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: C  126 SER cc_start: 0.8715 (t) cc_final: 0.8386 (m)
REVERT: C  131 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7811 (tt0)
REVERT: C  178 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8335 (mtpp)
REVERT: A   94 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6094 (pmt-80)
REVERT: A  232 MET cc_start: 0.8207 (ptt) cc_final: 0.7828 (ptt)
REVERT: A  268 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7556 (m-30)
REVERT: D   75 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7564 (t0)
REVERT: D  126 SER cc_start: 0.8709 (t) cc_final: 0.8284 (m)
REVERT: D  127 ASN cc_start: 0.8670 (p0) cc_final: 0.8240 (p0)
REVERT: D  178 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8488 (mtpp)
  outliers start: 61
  outliers final: 45
  residues processed: 280
  average time/residue: 0.1089
  time to fit residues: 38.1837
Evaluate side-chains
  297 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 244
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  157 HIS
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    0.2980
   chunk 56 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0050
   chunk 51 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 HIS
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.074039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.066708 restraints weight = 19003.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.068674 restraints weight = 8976.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.069937 restraints weight = 5052.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.070766 restraints weight = 3187.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.071332 restraints weight = 2202.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7278  Z= 0.142
  Angle     :  0.738  10.270   9894  Z= 0.364
  Chirality :  0.047   0.285   1114
  Planarity :  0.006   0.062   1276
  Dihedral  :  5.499  58.829   1002
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  9.59 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 32.43 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.28), residues: 886
  helix:  0.74 (0.28), residues: 342
  sheet:  0.21 (0.56), residues: 93
  loop : -2.19 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 117 
 TYR   0.012   0.001   TYR C  78 
 PHE   0.019   0.001   PHE B 143 
 TRP   0.007   0.001   TRP A 205 
 HIS   0.007   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7276)
  covalent geometry    : angle       0.73815 ( 9890)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       0.18683 (    4)
  hydrogen bonds       : bond        0.03611 (  256)
  hydrogen bonds       : angle       3.87060 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 251
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5835 (pmt-80)
REVERT: B  151 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7703 (ttm)
REVERT: B  160 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6965 (ptp-170)
REVERT: B  282 HIS cc_start: 0.8276 (m170) cc_final: 0.8074 (m170)
REVERT: C   28 MET cc_start: 0.5710 (pmm) cc_final: 0.5256 (pmm)
REVERT: C   54 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8185 (ptp-170)
REVERT: C   79 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: C   81 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8698 (ptmm)
REVERT: C  116 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8467 (ttmm)
REVERT: C  126 SER cc_start: 0.8673 (t) cc_final: 0.8331 (m)
REVERT: C  131 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7747 (tt0)
REVERT: A   94 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6010 (pmt-80)
REVERT: A  232 MET cc_start: 0.8163 (ptt) cc_final: 0.7789 (ptt)
REVERT: D   54 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8233 (ttp-170)
REVERT: D   75 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7372 (t0)
REVERT: D  105 ASN cc_start: 0.8499 (t0) cc_final: 0.8150 (t0)
REVERT: D  126 SER cc_start: 0.8658 (t) cc_final: 0.8227 (m)
REVERT: D  127 ASN cc_start: 0.8688 (p0) cc_final: 0.8165 (p0)
REVERT: D  178 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8495 (mtpp)
  outliers start: 55
  outliers final: 41
  residues processed: 286
  average time/residue: 0.1055
  time to fit residues: 37.8914
Evaluate side-chains
  287 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 239
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  160 ARG
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  109 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  157 HIS
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0270
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 HIS
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  43 HIS
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.071526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.064556 restraints weight = 19399.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.066407 restraints weight = 9111.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.067591 restraints weight = 5138.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.068393 restraints weight = 3254.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.068892 restraints weight = 2251.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7278  Z= 0.152
  Angle     :  0.790  10.272   9894  Z= 0.390
  Chirality :  0.047   0.293   1114
  Planarity :  0.006   0.063   1276
  Dihedral  :  5.384  57.891   1002
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  9.37 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 34.63 %
    Favored  : 59.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.28), residues: 886
  helix:  0.74 (0.28), residues: 349
  sheet:  0.20 (0.56), residues: 93
  loop : -2.28 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  46 
 TYR   0.015   0.001   TYR C  78 
 PHE   0.020   0.001   PHE B 164 
 TRP   0.006   0.001   TRP A 205 
 HIS   0.013   0.002   HIS A 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7276)
  covalent geometry    : angle       0.78981 ( 9890)
  SS BOND              : bond        0.00977 (    2)
  SS BOND              : angle       1.71841 (    4)
  hydrogen bonds       : bond        0.03676 (  256)
  hydrogen bonds       : angle       3.86924 (  732)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 246
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.5777 (pmt-80)
REVERT: B  101 TYR cc_start: 0.8912 (p90) cc_final: 0.8661 (p90)
REVERT: B  151 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7706 (ttm)
REVERT: B  160 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6977 (ptp-170)
REVERT: B  282 HIS cc_start: 0.8322 (m170) cc_final: 0.8106 (m170)
REVERT: C   28 MET cc_start: 0.5748 (pmm) cc_final: 0.5301 (pmm)
REVERT: C   79 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: C   81 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8669 (ptmm)
REVERT: C  126 SER cc_start: 0.8663 (t) cc_final: 0.8314 (m)
REVERT: C  131 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7772 (tt0)
REVERT: A   94 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.5937 (pmt-80)
REVERT: A  137 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7740 (tpp80)
REVERT: A  232 MET cc_start: 0.8174 (ptt) cc_final: 0.7785 (ptt)
REVERT: A  242 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8140 (mm-40)
REVERT: A  286 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6957 (mmm-85)
REVERT: D   36 ARG cc_start: 0.8712 (tpp80) cc_final: 0.8291 (mmm160)
REVERT: D   75 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7429 (t0)
REVERT: D  105 ASN cc_start: 0.8522 (t0) cc_final: 0.8190 (t0)
REVERT: D  126 SER cc_start: 0.8650 (t) cc_final: 0.8198 (m)
REVERT: D  127 ASN cc_start: 0.8694 (p0) cc_final: 0.8227 (p0)
REVERT: D  178 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8520 (mtpp)
  outliers start: 47
  outliers final: 36
  residues processed: 276
  average time/residue: 0.1108
  time to fit residues: 38.3794
Evaluate side-chains
  292 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 248
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  160 ARG
Chi-restraints excluded: chain B residue  178 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   94 ARG
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  291 PHE
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue  104 TYR
Chi-restraints excluded: chain D residue  109 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  157 HIS
Chi-restraints excluded: chain D residue  178 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0020
   chunk 34 optimal weight:    0.9990
   chunk 81 optimal weight:    0.1980
   chunk 62 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.3988

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

Flipped N/Q/H residues before XYZ refinement:
B  82 GLN
** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 HIS
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  43 HIS
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.076255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.069027 restraints weight = 19163.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.070956 restraints weight = 9098.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.072185 restraints weight = 5118.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.072987 restraints weight = 3226.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.073430 restraints weight = 2225.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   7278  Z= 0.151
  Angle     :  0.798  11.172   9894  Z= 0.394
  Chirality :  0.048   0.332   1114
  Planarity :  0.006   0.063   1276
  Dihedral  :  5.299  57.432   1001
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  9.71 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 34.88 %
    Favored  : 59.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.28), residues: 886
  helix:  0.66 (0.28), residues: 344
  sheet:  0.35 (0.56), residues: 91
  loop : -2.16 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  54 
 TYR   0.014   0.001   TYR C  78 
 PHE   0.018   0.001   PHE B 143 
 TRP   0.007   0.001   TRP D  97 
 HIS   0.008   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 7276)
  covalent geometry    : angle       0.79046 ( 9890)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       5.59852 (    4)
  hydrogen bonds       : bond        0.03562 (  256)
  hydrogen bonds       : angle       3.84223 (  732)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1360.71 seconds
wall clock time: 24 minutes 6.25 seconds (1446.25 seconds total)