Starting phenix.real_space_refine
on Sat Aug 23 18:07:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u8f_42023/08_2025/8u8f_42023_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u8f_42023/08_2025/8u8f_42023.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u8f_42023/08_2025/8u8f_42023.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u8f_42023/08_2025/8u8f_42023.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u8f_42023/08_2025/8u8f_42023_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u8f_42023/08_2025/8u8f_42023_trim.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4433      2.51       5
     N    1209      2.21       5
     O    1275      1.98       5
     H    6925      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13891
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 3800
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 5094
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "G"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 871
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 4094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4094
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 10, 'TRANS': 254}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 16
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
      Conformer: "B"
        Number of residues, atoms: 1, 16
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" CA APLM R 401 " occ=0.68
      ... (30 atoms not shown)
      pdb=" CF BPLM R 401 " occ=0.32
  Time building chain proxies: 2.52, per 1000 atoms: 0.18
  Number of scatterers: 13891
  At special positions: 0
  Unit cell: (78.26, 100.62, 126.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     O    1275      8.00
     N    1209      7.00
     C    4433      6.00
     H    6925      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 177 " - pdb=" SG  CYS R 184 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 304.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      46.1% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 38
      removed outlier: 3.552A  pdb=" N   LYS A  28 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 4.130A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.533A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.093A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.799A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.565A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 44 through 68
      removed outlier: 3.691A  pdb=" N   CYS R  48 " --> pdb=" O   ASP R  44 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU R  60 " --> pdb=" O   CYS R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 101
      removed outlier: 3.649A  pdb=" N   PHE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 140
      removed outlier: 3.610A  pdb=" N   SER R 109 " --> pdb=" O   SER R 105 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU R 110 " --> pdb=" O   ALA R 106 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL R 111 " --> pdb=" O   GLU R 107 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 142 through 146
      removed outlier: 4.059A  pdb=" N   TYR R 145 " --> pdb=" O   LEU R 142 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 170
      removed outlier: 4.035A  pdb=" N   LEU R 170 " --> pdb=" O   GLY R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 230
      removed outlier: 3.549A  pdb=" N   LEU R 229 " --> pdb=" O   GLN R 225 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN R 230 " --> pdb=" O   GLN R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 253
      removed outlier: 3.655A  pdb=" N   VAL R 251 " --> pdb=" O   ALA R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 254 through 270
      Proline residue:  R 262  - end of helix
    Processing helix  chain 'R' and resid 275 through 282
      removed outlier: 4.236A  pdb=" N   THR R 279 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR R 280 " --> pdb=" O   PRO R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 298
      removed outlier: 3.772A  pdb=" N   ALA R 286 " --> pdb=" O   THR R 282 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN R 289 " --> pdb=" O   PRO R 285 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   SER R 290 " --> pdb=" O   ALA R 286 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET R 291 " --> pdb=" O   THR R 287 " (cutoff:3.500A)
      Proline residue:  R 294  - end of helix
    Processing helix  chain 'R' and resid 301 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.518A  pdb=" N   PHE A 208 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 3.790A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.901A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.533A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.627A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.857A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.837A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.484A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.55

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6897
        1.04 -     1.23: 246
        1.23 -     1.43: 2748
        1.43 -     1.63: 4065
        1.63 -     1.83: 68
  Bond restraints: 14024
  Sorted by residual:
  bond pdb=" N   VAL R 132 "
       pdb=" CA  VAL R 132 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.30e-02 5.92e+03 8.90e+00
  bond pdb=" N   LEU R 136 "
       pdb=" H   LEU R 136 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.83e+00
  bond pdb=" N   ALA R 129 "
       pdb=" H   ALA R 129 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.74e+00
  bond pdb=" N   VAL R 155 "
       pdb=" H   VAL R 155 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.73e+00
  bond pdb=" N   LEU R  78 "
       pdb=" H   LEU R  78 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.70e+00
  ... (remaining 14019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.09: 25239
        7.09 -    14.18: 2
       14.18 -    21.27: 0
       21.27 -    28.36: 0
       28.36 -    35.45: 3
  Bond angle restraints: 25244
  Sorted by residual:
  angle pdb=" C   ASN B 340 "
        pdb=" CA  ASN B 340 "
        pdb=" HA  ASN B 340 "
      ideal   model   delta    sigma   weight residual
     109.00   73.55   35.45 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" N   ASN B 340 "
        pdb=" CA  ASN B 340 "
        pdb=" HA  ASN B 340 "
      ideal   model   delta    sigma   weight residual
     110.00   74.70   35.30 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" CB  ASN B 340 "
        pdb=" CA  ASN B 340 "
        pdb=" HA  ASN B 340 "
      ideal   model   delta    sigma   weight residual
     109.00   79.73   29.27 3.00e+00 1.11e-01 9.52e+01
  angle pdb=" CA  PRO G  49 "
        pdb=" N   PRO G  49 "
        pdb=" CD  PRO G  49 "
      ideal   model   delta    sigma   weight residual
     112.00  104.99    7.01 1.40e+00 5.10e-01 2.51e+01
  angle pdb=" N   ASN B 313 "
        pdb=" CA  ASN B 313 "
        pdb=" CB  ASN B 313 "
      ideal   model   delta    sigma   weight residual
     114.17  109.59    4.58 1.14e+00 7.69e-01 1.62e+01
  ... (remaining 25239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5908
       17.91 -    35.83: 502
       35.83 -    53.74: 143
       53.74 -    71.66: 36
       71.66 -    89.57: 14
  Dihedral angle restraints: 6603
    sinusoidal: 3564
      harmonic: 3039
  Sorted by residual:
  dihedral pdb=" CB  CYS R 177 "
           pdb=" SG  CYS R 177 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -26.65  -59.35     1      1.00e+01 1.00e-02 4.71e+01
  dihedral pdb=" CA  ASN R 176 "
           pdb=" C   ASN R 176 "
           pdb=" N   CYS R 177 "
           pdb=" CA  CYS R 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.38   21.62     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  VAL R 187 "
           pdb=" C   VAL R 187 "
           pdb=" N   TYR R 188 "
           pdb=" CA  TYR R 188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 6600 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1050
       0.091 -    0.182: 53
       0.182 -    0.273: 0
       0.273 -    0.364: 0
       0.364 -    0.455: 1
  Chirality restraints: 1104
  Sorted by residual:
  chirality pdb=" CA  ASN B 340 "
            pdb=" N   ASN B 340 "
            pdb=" C   ASN B 340 "
            pdb=" CB  ASN B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.17e+00
  chirality pdb=" CA  VAL R 155 "
            pdb=" N   VAL R 155 "
            pdb=" C   VAL R 155 "
            pdb=" CB  VAL R 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  LEU R 159 "
            pdb=" N   LEU R 159 "
            pdb=" C   LEU R 159 "
            pdb=" CB  LEU R 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1101 not shown)

  Planarity restraints: 2076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 152 "    0.447 9.50e-02 1.11e+02   1.51e-01 3.60e+01
        pdb=" NE  ARG R 152 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 152 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 152 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 152 "   -0.005 2.00e-02 2.50e+03
        pdb="HH11 ARG R 152 "   -0.048 2.00e-02 2.50e+03
        pdb="HH12 ARG R 152 "    0.051 2.00e-02 2.50e+03
        pdb="HH21 ARG R 152 "    0.011 2.00e-02 2.50e+03
        pdb="HH22 ARG R 152 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.085 5.00e-02 4.00e+02   1.25e-01 2.51e+01
        pdb=" N   PRO G  49 "   -0.217 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 136 "    0.013 2.00e-02 2.50e+03   2.41e-02 5.82e+00
        pdb=" N   SER R 137 "   -0.042 2.00e-02 2.50e+03
        pdb=" CA  SER R 137 "    0.011 2.00e-02 2.50e+03
        pdb=" H   SER R 137 "    0.018 2.00e-02 2.50e+03
  ... (remaining 2073 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 912
        2.20 -     2.80: 28548
        2.80 -     3.40: 38690
        3.40 -     4.00: 49337
        4.00 -     4.60: 76825
  Nonbonded interactions: 194312
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN R 176 "
            pdb=" H   SER R 191 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" O   ASN R 140 "
            pdb=" H   TYR R 144 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" OD1 ASP R 179 "
            pdb=" H   LEU R 181 "
     model   vdw
     1.662 2.450
  nonbonded pdb="HH21 ARG A  38 "
            pdb=" OE2 GLU R 147 "
     model   vdw
     1.666 2.450
  nonbonded pdb=" H   PHE B 235 "
            pdb=" O   ALA B 240 "
     model   vdw
     1.666 2.450
  ... (remaining 194307 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.800
  Find NCS groups from input model:        0.030
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   7100  Z= 0.172
  Angle     :  0.545  10.634   9618  Z= 0.326
  Chirality :  0.042   0.455   1104
  Planarity :  0.007   0.182   1219
  Dihedral  : 15.464  89.571   2563
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.51 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 19.46 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.30), residues: 875
  helix:  2.63 (0.28), residues: 358
  sheet:  0.14 (0.42), residues: 156
  loop : -0.42 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  42 
 TYR   0.024   0.001   TYR R 139 
 PHE   0.013   0.001   PHE R 299 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.002   0.000   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7099)
  covalent geometry    : angle       0.54445 ( 9616)
  SS BOND              : bond        0.01154 (    1)
  SS BOND              : angle       1.38070 (    2)
  hydrogen bonds       : bond        0.17459 (  363)
  hydrogen bonds       : angle       7.02043 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 139
  average time/residue: 0.1814
  time to fit residues: 32.7073
Evaluate side-chains
  132 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.190158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.154515 restraints weight = 24608.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 3.05
r_work: 0.3779 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3781 r_free = 0.3781    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3781 r_free = 0.3781    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7100  Z= 0.162
  Angle     :  0.535  10.142   9618  Z= 0.290
  Chirality :  0.042   0.437   1104
  Planarity :  0.005   0.077   1219
  Dihedral  :  4.600  52.072    992
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.11 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.26 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.30), residues: 875
  helix:  2.56 (0.27), residues: 368
  sheet: -0.51 (0.43), residues: 161
  loop : -0.66 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.011   0.001   TYR B 124 
 PHE   0.019   0.002   PHE B 241 
 TRP   0.017   0.001   TRP B  63 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7099)
  covalent geometry    : angle       0.53401 ( 9616)
  SS BOND              : bond        0.01200 (    1)
  SS BOND              : angle       2.08478 (    2)
  hydrogen bonds       : bond        0.04723 (  363)
  hydrogen bonds       : angle       4.94474 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 TRP cc_start: 0.7399 (m-10) cc_final: 0.7137 (m-10)
REVERT: G   17 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8152 (mm-30)
REVERT: R   56 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6973 (m)
REVERT: R  179 ASP cc_start: 0.6970 (p0) cc_final: 0.6495 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 147
  average time/residue: 0.1938
  time to fit residues: 36.8232
Evaluate side-chains
  141 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.190739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.154670 restraints weight = 24640.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 3.08
r_work: 0.3779 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7100  Z= 0.115
  Angle     :  0.488  10.201   9618  Z= 0.260
  Chirality :  0.041   0.445   1104
  Planarity :  0.004   0.067   1219
  Dihedral  :  4.402  50.498    992
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.20 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.85 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.30), residues: 875
  helix:  2.67 (0.27), residues: 367
  sheet: -0.91 (0.40), residues: 172
  loop : -0.65 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 218 
 TYR   0.013   0.001   TYR A 311 
 PHE   0.013   0.001   PHE A 246 
 TRP   0.013   0.001   TRP B  63 
 HIS   0.002   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7099)
  covalent geometry    : angle       0.48755 ( 9616)
  SS BOND              : bond        0.01098 (    1)
  SS BOND              : angle       1.84271 (    2)
  hydrogen bonds       : bond        0.04119 (  363)
  hydrogen bonds       : angle       4.55955 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 TRP cc_start: 0.7446 (m-10) cc_final: 0.7117 (m-10)
REVERT: B  258 ASP cc_start: 0.7114 (t70) cc_final: 0.6654 (t70)
REVERT: G   13 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8146 (ttm110)
REVERT: G   17 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8183 (mm-30)
REVERT: R   56 CYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6966 (m)
REVERT: R  204 MET cc_start: 0.7345 (ttm) cc_final: 0.7133 (mtp)
  outliers start: 21
  outliers final: 13
  residues processed: 153
  average time/residue: 0.1825
  time to fit residues: 36.0403
Evaluate side-chains
  146 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 85 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.193166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.159723 restraints weight = 23633.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.64
r_work: 0.3820 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7100  Z= 0.134
  Angle     :  0.503  10.218   9618  Z= 0.269
  Chirality :  0.041   0.442   1104
  Planarity :  0.004   0.063   1219
  Dihedral  :  4.595  49.307    992
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.11 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.93 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.30), residues: 875
  helix:  2.65 (0.27), residues: 367
  sheet: -1.14 (0.41), residues: 167
  loop : -0.76 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 218 
 TYR   0.008   0.001   TYR A 311 
 PHE   0.016   0.001   PHE B 241 
 TRP   0.012   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7099)
  covalent geometry    : angle       0.50199 ( 9616)
  SS BOND              : bond        0.00983 (    1)
  SS BOND              : angle       2.02814 (    2)
  hydrogen bonds       : bond        0.04027 (  363)
  hydrogen bonds       : angle       4.46738 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 TRP cc_start: 0.7514 (m-10) cc_final: 0.7077 (m-10)
REVERT: B  217 MET cc_start: 0.7795 (mtm) cc_final: 0.7041 (mmp)
REVERT: G   17 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8239 (mm-30)
REVERT: R   56 CYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7068 (m)
REVERT: R  204 MET cc_start: 0.7562 (ttm) cc_final: 0.7349 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 146
  average time/residue: 0.1845
  time to fit residues: 34.5775
Evaluate side-chains
  154 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    1.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.188283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.154491 restraints weight = 24153.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 2.64
r_work: 0.3743 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7100  Z= 0.189
  Angle     :  0.562  10.178   9618  Z= 0.304
  Chirality :  0.042   0.438   1104
  Planarity :  0.004   0.062   1219
  Dihedral  :  5.121  47.859    992
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.14 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.60 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.29), residues: 875
  helix:  2.34 (0.27), residues: 367
  sheet: -1.50 (0.40), residues: 170
  loop : -0.92 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 218 
 TYR   0.014   0.001   TYR A 311 
 PHE   0.025   0.002   PHE B 241 
 TRP   0.017   0.002   TRP B  63 
 HIS   0.005   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 7099)
  covalent geometry    : angle       0.56104 ( 9616)
  SS BOND              : bond        0.01025 (    1)
  SS BOND              : angle       2.51931 (    2)
  hydrogen bonds       : bond        0.04426 (  363)
  hydrogen bonds       : angle       4.60799 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8325 (tp40) cc_final: 0.7977 (tp40)
REVERT: A  358 TYR cc_start: 0.8055 (m-80) cc_final: 0.7754 (m-80)
REVERT: B   44 GLN cc_start: 0.7382 (mt0) cc_final: 0.7105 (mt0)
REVERT: B   63 TRP cc_start: 0.7375 (m-10) cc_final: 0.6830 (m-10)
REVERT: B  258 ASP cc_start: 0.7351 (t70) cc_final: 0.6753 (t0)
REVERT: B  262 MET cc_start: 0.7573 (tpp) cc_final: 0.7267 (tpp)
REVERT: G   13 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8043 (ttm110)
REVERT: G   17 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8159 (mm-30)
REVERT: R   56 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7145 (m)
REVERT: R  204 MET cc_start: 0.7497 (ttm) cc_final: 0.7267 (mtp)
  outliers start: 26
  outliers final: 22
  residues processed: 149
  average time/residue: 0.1929
  time to fit residues: 37.2531
Evaluate side-chains
  149 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  179 ASP
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.188445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.154843 restraints weight = 23793.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 2.63
r_work: 0.3769 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7100  Z= 0.162
  Angle     :  0.534   9.994   9618  Z= 0.287
  Chirality :  0.042   0.436   1104
  Planarity :  0.004   0.062   1219
  Dihedral  :  5.007  46.737    992
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.91 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.00 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.29), residues: 875
  helix:  2.32 (0.27), residues: 366
  sheet: -1.73 (0.40), residues: 165
  loop : -0.96 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 218 
 TYR   0.012   0.001   TYR A 311 
 PHE   0.019   0.002   PHE B 241 
 TRP   0.013   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7099)
  covalent geometry    : angle       0.53285 ( 9616)
  SS BOND              : bond        0.00942 (    1)
  SS BOND              : angle       2.15884 (    2)
  hydrogen bonds       : bond        0.04181 (  363)
  hydrogen bonds       : angle       4.51846 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 TYR cc_start: 0.8138 (m-80) cc_final: 0.7847 (m-80)
REVERT: B   63 TRP cc_start: 0.7493 (m-10) cc_final: 0.6954 (m-10)
REVERT: B  171 ILE cc_start: 0.7175 (mm) cc_final: 0.6858 (mm)
REVERT: B  262 MET cc_start: 0.7684 (tpp) cc_final: 0.7480 (tpp)
REVERT: R   56 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7148 (m)
REVERT: R  204 MET cc_start: 0.7595 (ttm) cc_final: 0.7368 (mtp)
  outliers start: 25
  outliers final: 20
  residues processed: 147
  average time/residue: 0.1672
  time to fit residues: 31.8933
Evaluate side-chains
  152 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.188380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.154694 restraints weight = 23800.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.63
r_work: 0.3765 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3592 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7100  Z= 0.161
  Angle     :  0.539   9.961   9618  Z= 0.291
  Chirality :  0.042   0.436   1104
  Planarity :  0.004   0.059   1219
  Dihedral  :  5.038  46.621    992
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.26 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.54 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.29), residues: 875
  helix:  2.27 (0.27), residues: 367
  sheet: -1.72 (0.40), residues: 161
  loop : -1.09 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 218 
 TYR   0.012   0.001   TYR A 311 
 PHE   0.019   0.002   PHE B 241 
 TRP   0.014   0.002   TRP A 281 
 HIS   0.004   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7099)
  covalent geometry    : angle       0.53758 ( 9616)
  SS BOND              : bond        0.02068 (    1)
  SS BOND              : angle       2.27219 (    2)
  hydrogen bonds       : bond        0.04161 (  363)
  hydrogen bonds       : angle       4.52100 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 TYR cc_start: 0.8169 (m-80) cc_final: 0.7866 (m-80)
REVERT: B   63 TRP cc_start: 0.7540 (m-10) cc_final: 0.6938 (m-10)
REVERT: B  171 ILE cc_start: 0.7139 (mm) cc_final: 0.6760 (mm)
REVERT: B  217 MET cc_start: 0.7698 (mtm) cc_final: 0.6919 (mmp)
REVERT: R   56 CYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7126 (m)
REVERT: R  108 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7104 (tpp)
REVERT: R  204 MET cc_start: 0.7560 (ttm) cc_final: 0.7333 (mtp)
  outliers start: 24
  outliers final: 22
  residues processed: 145
  average time/residue: 0.2216
  time to fit residues: 41.0986
Evaluate side-chains
  152 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 57 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0030
   chunk 85 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.190400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.156781 restraints weight = 23763.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.62
r_work: 0.3785 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7100  Z= 0.127
  Angle     :  0.514  10.026   9618  Z= 0.275
  Chirality :  0.041   0.439   1104
  Planarity :  0.004   0.057   1219
  Dihedral  :  4.833  46.020    992
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.67 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.29), residues: 875
  helix:  2.41 (0.27), residues: 367
  sheet: -1.66 (0.41), residues: 161
  loop : -1.06 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 218 
 TYR   0.012   0.001   TYR A 311 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.013   0.001   TRP A 281 
 HIS   0.003   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7099)
  covalent geometry    : angle       0.51314 ( 9616)
  SS BOND              : bond        0.01756 (    1)
  SS BOND              : angle       2.16092 (    2)
  hydrogen bonds       : bond        0.03887 (  363)
  hydrogen bonds       : angle       4.39831 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  158 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 TYR cc_start: 0.8140 (m-80) cc_final: 0.7851 (m-80)
REVERT: B   63 TRP cc_start: 0.7494 (m-10) cc_final: 0.6842 (m-10)
REVERT: B  217 MET cc_start: 0.7701 (mtm) cc_final: 0.6920 (mmp)
REVERT: B  258 ASP cc_start: 0.7376 (t70) cc_final: 0.6829 (t0)
REVERT: R   56 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7196 (m)
REVERT: R  108 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7080 (tpp)
REVERT: R  147 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7194 (tp30)
REVERT: R  204 MET cc_start: 0.7579 (ttm) cc_final: 0.7346 (mtp)
  outliers start: 25
  outliers final: 23
  residues processed: 148
  average time/residue: 0.2438
  time to fit residues: 46.0766
Evaluate side-chains
  153 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 83 optimal weight:    0.1980
   chunk 73 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.190476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.156725 restraints weight = 23899.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 2.66
r_work: 0.3757 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7100  Z= 0.125
  Angle     :  0.518  10.014   9618  Z= 0.277
  Chirality :  0.041   0.439   1104
  Planarity :  0.004   0.078   1219
  Dihedral  :  4.797  45.987    992
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.81 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.29), residues: 875
  helix:  2.53 (0.27), residues: 366
  sheet: -1.63 (0.41), residues: 161
  loop : -1.02 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 218 
 TYR   0.012   0.001   TYR A 311 
 PHE   0.015   0.001   PHE A 290 
 TRP   0.015   0.001   TRP A 281 
 HIS   0.003   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7099)
  covalent geometry    : angle       0.51689 ( 9616)
  SS BOND              : bond        0.01447 (    1)
  SS BOND              : angle       2.08022 (    2)
  hydrogen bonds       : bond        0.03836 (  363)
  hydrogen bonds       : angle       4.35802 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 TYR cc_start: 0.8039 (m-80) cc_final: 0.7751 (m-80)
REVERT: B   63 TRP cc_start: 0.7375 (m-10) cc_final: 0.6762 (m-10)
REVERT: B  217 MET cc_start: 0.7500 (mtm) cc_final: 0.6798 (mmp)
REVERT: R   56 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7205 (m)
REVERT: R  108 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6952 (tpp)
REVERT: R  139 TYR cc_start: 0.8254 (t80) cc_final: 0.7841 (t80)
REVERT: R  204 MET cc_start: 0.7413 (ttm) cc_final: 0.7200 (mtp)
  outliers start: 24
  outliers final: 21
  residues processed: 143
  average time/residue: 0.2190
  time to fit residues: 40.4238
Evaluate side-chains
  151 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 22 optimal weight:    0.3980
   overall best weight:    1.4186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.188726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.154975 restraints weight = 23795.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 2.63
r_work: 0.3764 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7100  Z= 0.156
  Angle     :  0.538  10.033   9618  Z= 0.290
  Chirality :  0.041   0.437   1104
  Planarity :  0.005   0.076   1219
  Dihedral  :  4.936  45.543    992
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.81 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.29), residues: 875
  helix:  2.43 (0.27), residues: 367
  sheet: -1.68 (0.41), residues: 161
  loop : -1.11 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  38 
 TYR   0.013   0.001   TYR A 311 
 PHE   0.019   0.002   PHE B 241 
 TRP   0.017   0.001   TRP A 281 
 HIS   0.004   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7099)
  covalent geometry    : angle       0.53668 ( 9616)
  SS BOND              : bond        0.01411 (    1)
  SS BOND              : angle       2.25469 (    2)
  hydrogen bonds       : bond        0.04003 (  363)
  hydrogen bonds       : angle       4.46180 ( 1053)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 TRP cc_start: 0.7530 (m-10) cc_final: 0.6894 (m-10)
REVERT: B  217 MET cc_start: 0.7755 (mtm) cc_final: 0.6962 (mmp)
REVERT: R   56 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7158 (m)
REVERT: R  108 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7098 (tpp)
REVERT: R  139 TYR cc_start: 0.8415 (t80) cc_final: 0.8011 (t80)
REVERT: R  204 MET cc_start: 0.7595 (ttm) cc_final: 0.7375 (mtp)
  outliers start: 25
  outliers final: 23
  residues processed: 148
  average time/residue: 0.2164
  time to fit residues: 41.6797
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 35 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.191819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.158235 restraints weight = 23684.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 2.63
r_work: 0.3798 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7100  Z= 0.110
  Angle     :  0.502  10.071   9618  Z= 0.267
  Chirality :  0.041   0.443   1104
  Planarity :  0.004   0.079   1219
  Dihedral  :  4.672  45.367    992
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.07 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.30), residues: 875
  helix:  2.65 (0.27), residues: 367
  sheet: -1.53 (0.41), residues: 166
  loop : -0.96 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 218 
 TYR   0.012   0.001   TYR A 311 
 PHE   0.015   0.001   PHE A 290 
 TRP   0.017   0.001   TRP A 281 
 HIS   0.002   0.001   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7099)
  covalent geometry    : angle       0.50110 ( 9616)
  SS BOND              : bond        0.01318 (    1)
  SS BOND              : angle       1.71277 (    2)
  hydrogen bonds       : bond        0.03722 (  363)
  hydrogen bonds       : angle       4.29566 ( 1053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3617.28 seconds
wall clock time: 62 minutes 0.35 seconds (3720.35 seconds total)