Starting phenix.real_space_refine
on Sun Apr  5 05:39:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m3q_63606/04_2026/9m3q_63606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m3q_63606/04_2026/9m3q_63606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m3q_63606/04_2026/9m3q_63606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m3q_63606/04_2026/9m3q_63606.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m3q_63606/04_2026/9m3q_63606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m3q_63606/04_2026/9m3q_63606.map"
  }
  resolution = 2.74
  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=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5374      2.51       5
     N    1451      2.21       5
     O    1575      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8455
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2516
          Classifications: {'peptide': 318}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 304}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "A"
      Number of atoms: 1926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1926
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SPD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.61, per 1000 atoms: 0.19
  Number of scatterers: 8455
  At special positions: 0
  Unit cell: (76.544, 99.84, 137.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1575      8.00
     N    1451      7.00
     C    5374      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  14 " - pdb=" SG  CYS R  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  22 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=1.79

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 318.7 milliseconds
  

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      43.3% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 28 through 60
    Processing helix  chain 'R' and resid 61 through 64
    Processing helix  chain 'R' and resid 65 through 95
      removed outlier: 4.435A  pdb=" N   MET R  86 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      Proline residue:  R  87  - end of helix
      removed outlier: 3.721A  pdb=" N   ILE R  91 " --> pdb=" O   PRO R  87 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 136
    Processing helix  chain 'R' and resid 139 through 144
    Processing helix  chain 'R' and resid 145 through 168
    Processing helix  chain 'R' and resid 171 through 175
      removed outlier: 3.519A  pdb=" N   LEU R 174 " --> pdb=" O   LYS R 171 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU R 175 " --> pdb=" O   ALA R 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 171 through 175'
    Processing helix  chain 'R' and resid 177 through 184
    Processing helix  chain 'R' and resid 195 through 206
    Processing helix  chain 'R' and resid 207 through 235
    Processing helix  chain 'R' and resid 251 through 269
      removed outlier: 3.955A  pdb=" N   VAL R 261 " --> pdb=" O   THR R 257 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL R 262 " --> pdb=" O   LEU R 258 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE R 265 " --> pdb=" O   VAL R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 279
    Processing helix  chain 'R' and resid 280 through 283
      removed outlier: 3.762A  pdb=" N   ASN R 283 " --> pdb=" O   PRO R 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 280 through 283'
    Processing helix  chain 'R' and resid 287 through 310
      removed outlier: 3.702A  pdb=" N   ASN R 301 " --> pdb=" O   LEU R 297 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER R 302 " --> pdb=" O   GLY R 298 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 325
    Processing helix  chain 'R' and resid 326 through 330
      removed outlier: 3.596A  pdb=" N   PHE R 329 " --> pdb=" O   LEU R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 332 through 336
      removed outlier: 3.783A  pdb=" N   ASP R 335 " --> pdb=" O   ASN R 332 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE R 336 " --> pdb=" O   SER R 333 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 332 through 336'
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.507A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.717A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.615A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 37
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 95 through 100
    Processing helix  chain 'A' and resid 114 through 116
      No H-bonds generated for 'chain 'A' and resid 114 through 116'
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.636A  pdb=" N   GLY A 156 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 163
      removed outlier: 3.611A  pdb=" N   ASP A 162 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 205
      removed outlier: 4.105A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER A 201 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.564A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.826A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.646A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.857A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.697A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.543A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.545A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 6 through 7
    Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.866A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 4.720A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   VAL A 139 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   HIS A 214 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1221 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: 1.49

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2751
        1.35 -     1.47: 2048
        1.47 -     1.58: 3761
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8638
  Sorted by residual:
  bond pdb=" CA  SER N  54 "
       pdb=" CB  SER N  54 "
    ideal  model  delta    sigma   weight residual
    1.536  1.483  0.053 1.46e-02 4.69e+03 1.34e+01
  bond pdb=" CA  SER R 199 "
       pdb=" CB  SER R 199 "
    ideal  model  delta    sigma   weight residual
    1.529  1.478  0.051 1.58e-02 4.01e+03 1.03e+01
  bond pdb=" CA  SER N  52 "
       pdb=" CB  SER N  52 "
    ideal  model  delta    sigma   weight residual
    1.527  1.481  0.046 1.44e-02 4.82e+03 1.01e+01
  bond pdb=" N   ASP B 163 "
       pdb=" CA  ASP B 163 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.039 1.25e-02 6.40e+03 9.81e+00
  bond pdb=" N   ILE R 124 "
       pdb=" CA  ILE R 124 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.74e+00
  ... (remaining 8633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 11420
        2.30 -     4.61: 267
        4.61 -     6.91: 26
        6.91 -     9.22: 2
        9.22 -    11.52: 1
  Bond angle restraints: 11716
  Sorted by residual:
  angle pdb=" N   LEU R 297 "
        pdb=" CA  LEU R 297 "
        pdb=" C   LEU R 297 "
      ideal   model   delta    sigma   weight residual
     112.38  103.60    8.78 1.22e+00 6.72e-01 5.17e+01
  angle pdb=" N   LEU R 204 "
        pdb=" CA  LEU R 204 "
        pdb=" C   LEU R 204 "
      ideal   model   delta    sigma   weight residual
     113.97  108.22    5.75 1.28e+00 6.10e-01 2.02e+01
  angle pdb=" N   LEU R 205 "
        pdb=" CA  LEU R 205 "
        pdb=" C   LEU R 205 "
      ideal   model   delta    sigma   weight residual
     113.38  107.88    5.50 1.23e+00 6.61e-01 2.00e+01
  angle pdb=" N   ASP B 323 "
        pdb=" CA  ASP B 323 "
        pdb=" C   ASP B 323 "
      ideal   model   delta    sigma   weight residual
     113.38  108.00    5.38 1.23e+00 6.61e-01 1.91e+01
  angle pdb=" C   HIS R  27 "
        pdb=" CA  HIS R  27 "
        pdb=" CB  HIS R  27 "
      ideal   model   delta    sigma   weight residual
     116.54  111.74    4.80 1.15e+00 7.56e-01 1.75e+01
  ... (remaining 11711 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.52: 4626
       15.52 -    31.03: 391
       31.03 -    46.55: 79
       46.55 -    62.07: 21
       62.07 -    77.59: 7
  Dihedral angle restraints: 5124
    sinusoidal: 1996
      harmonic: 3128
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -8.41  -77.59     1      1.00e+01 1.00e-02 7.54e+01
  dihedral pdb=" CB  CYS R  22 "
           pdb=" SG  CYS R  22 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.93   54.93     1      1.00e+01 1.00e-02 4.08e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.08  -25.92     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 974
       0.050 -    0.100: 254
       0.100 -    0.150: 72
       0.150 -    0.201: 21
       0.201 -    0.251: 2
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  VAL B 112 "
            pdb=" N   VAL B 112 "
            pdb=" C   VAL B 112 "
            pdb=" CB  VAL B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  LEU B  79 "
            pdb=" N   LEU B  79 "
            pdb=" C   LEU B  79 "
            pdb=" CB  LEU B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  VAL R 200 "
            pdb=" N   VAL R 200 "
            pdb=" C   VAL R 200 "
            pdb=" CB  VAL R 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.95e-01
  ... (remaining 1320 not shown)

  Planarity restraints: 1492
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 237 "    0.473 9.50e-02 1.11e+02   2.12e-01 2.75e+01
        pdb=" NE  ARG A 237 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 237 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 237 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 237 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N  72 "    0.434 9.50e-02 1.11e+02   1.95e-01 2.32e+01
        pdb=" NE  ARG N  72 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG N  72 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG N  72 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG N  72 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 196 "    0.020 2.00e-02 2.50e+03   3.95e-02 1.56e+01
        pdb=" C   ALA R 196 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ALA R 196 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU R 197 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1489 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1413
        2.76 -     3.30: 8255
        3.30 -     3.83: 14592
        3.83 -     4.37: 17355
        4.37 -     4.90: 30216
  Nonbonded interactions: 71831
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" ND2 ASN A  50 "
            pdb=" OD2 ASP A 114 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OG  SER B 279 "
            pdb=" OD1 ASP C  48 "
     model   vdw
     2.341 3.040
  ... (remaining 71826 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=1.00 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:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.120
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.239   8643  Z= 0.349
  Angle     :  0.756  11.521  11726  Z= 0.496
  Chirality :  0.052   0.251   1323
  Planarity :  0.010   0.212   1492
  Dihedral  : 12.431  72.762   3089
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.53 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.27), residues: 1061
  helix:  1.31 (0.27), residues: 421
  sheet: -0.80 (0.32), residues: 239
  loop : -0.66 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  61 
 TYR   0.018   0.001   TYR R 163 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.013   0.001   TRP A  96 
 HIS   0.005   0.001   HIS R  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 8638)
  covalent geometry    : angle       0.74752 (11716)
  SS BOND              : bond        0.10674 (    5)
  SS BOND              : angle       3.94556 (   10)
  hydrogen bonds       : bond        0.16493 (  424)
  hydrogen bonds       : angle       6.51861 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   51 SER cc_start: 0.8019 (p) cc_final: 0.7703 (p)
REVERT: R  106 LEU cc_start: 0.7780 (tp) cc_final: 0.7422 (tp)
REVERT: R  174 LEU cc_start: 0.8184 (mt) cc_final: 0.7983 (mt)
REVERT: R  205 LEU cc_start: 0.8122 (tp) cc_final: 0.7875 (tp)
REVERT: R  267 LEU cc_start: 0.7618 (mm) cc_final: 0.7395 (mm)
REVERT: R  312 PHE cc_start: 0.8147 (t80) cc_final: 0.7756 (t80)
REVERT: B   76 ASP cc_start: 0.6938 (t70) cc_final: 0.6622 (t70)
REVERT: B  217 MET cc_start: 0.7032 (ppp) cc_final: 0.6797 (ppp)
REVERT: N   52 SER cc_start: 0.8060 (t) cc_final: 0.7727 (m)
REVERT: N   57 SER cc_start: 0.7813 (p) cc_final: 0.7223 (p)
REVERT: A  102 ASP cc_start: 0.6947 (p0) cc_final: 0.6725 (p0)
REVERT: A  145 LYS cc_start: 0.8164 (mttt) cc_final: 0.7959 (mttm)
REVERT: A  147 ASP cc_start: 0.7614 (p0) cc_final: 0.7218 (p0)
REVERT: A  159 LYS cc_start: 0.8064 (mmpt) cc_final: 0.7691 (mmpt)
REVERT: A  244 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6620 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.5191
  time to fit residues: 137.4310
Evaluate side-chains
  227 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
R  64 GLN
B  13 GLN
B  75 GLN
B 239 ASN
N  35 ASN
N  53 GLN
N  82 GLN
A  28 ASN
A 130 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.129766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.115035 restraints weight = 11565.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.82
r_work: 0.3459 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8643  Z= 0.241
  Angle     :  0.585  11.002  11726  Z= 0.310
  Chirality :  0.045   0.153   1323
  Planarity :  0.005   0.062   1492
  Dihedral  :  4.388  28.001   1177
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  9.80 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.26), residues: 1061
  helix:  1.67 (0.26), residues: 423
  sheet: -0.64 (0.32), residues: 235
  loop : -0.65 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 117 
 TYR   0.011   0.001   TYR R 163 
 PHE   0.024   0.002   PHE N  68 
 TRP   0.016   0.002   TRP A  96 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 8638)
  covalent geometry    : angle       0.58408 (11716)
  SS BOND              : bond        0.00179 (    5)
  SS BOND              : angle       1.40606 (   10)
  hydrogen bonds       : bond        0.04442 (  424)
  hydrogen bonds       : angle       4.94098 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 241
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: R   36 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7456 (m-80)
REVERT: R  106 LEU cc_start: 0.8012 (tp) cc_final: 0.7736 (tp)
REVERT: R  267 LEU cc_start: 0.8101 (mm) cc_final: 0.7861 (mm)
REVERT: R  284 PHE cc_start: 0.8163 (m-80) cc_final: 0.7854 (m-80)
REVERT: R  312 PHE cc_start: 0.8528 (t80) cc_final: 0.7995 (t80)
REVERT: B   14 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8465 (mt)
REVERT: B   76 ASP cc_start: 0.7543 (t70) cc_final: 0.7249 (t70)
REVERT: B  256 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7892 (mtm180)
REVERT: N   52 SER cc_start: 0.8392 (t) cc_final: 0.8181 (t)
REVERT: A   73 LYS cc_start: 0.8211 (mttm) cc_final: 0.7912 (mttm)
REVERT: A   93 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8274 (mtm180)
REVERT: A  159 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7567 (mmpt)
REVERT: A  162 ASP cc_start: 0.7893 (m-30) cc_final: 0.7661 (m-30)
  outliers start: 23
  outliers final: 5
  residues processed: 248
  average time/residue: 0.5037
  time to fit residues: 133.1283
Evaluate side-chains
  237 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 228
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 TYR
Chi-restraints excluded: chain R residue  170 SER
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain A residue   93 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 95 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 229 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.131029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.116345 restraints weight = 11446.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.81
r_work: 0.3482 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8643  Z= 0.132
  Angle     :  0.519  11.046  11726  Z= 0.273
  Chirality :  0.042   0.151   1323
  Planarity :  0.004   0.058   1492
  Dihedral  :  4.182  27.046   1177
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.64 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.27), residues: 1061
  helix:  1.99 (0.26), residues: 424
  sheet: -0.52 (0.32), residues: 234
  loop : -0.59 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  61 
 TYR   0.009   0.001   TYR R 100 
 PHE   0.012   0.001   PHE N  68 
 TRP   0.017   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8638)
  covalent geometry    : angle       0.51858 (11716)
  SS BOND              : bond        0.00152 (    5)
  SS BOND              : angle       1.03178 (   10)
  hydrogen bonds       : bond        0.03766 (  424)
  hydrogen bonds       : angle       4.67175 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   39 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8210 (mp)
REVERT: R  106 LEU cc_start: 0.7936 (tp) cc_final: 0.7701 (tt)
REVERT: R  152 MET cc_start: 0.7975 (mtp) cc_final: 0.7774 (mtm)
REVERT: R  215 VAL cc_start: 0.8469 (t) cc_final: 0.8143 (m)
REVERT: R  267 LEU cc_start: 0.8055 (mm) cc_final: 0.7784 (mm)
REVERT: R  284 PHE cc_start: 0.8147 (m-80) cc_final: 0.7782 (m-80)
REVERT: B   19 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7619 (ttp-110)
REVERT: B  228 ASP cc_start: 0.7524 (m-30) cc_final: 0.7162 (m-30)
REVERT: N   52 SER cc_start: 0.8363 (t) cc_final: 0.8121 (t)
REVERT: A   61 ARG cc_start: 0.6744 (ttm110) cc_final: 0.6150 (mtp85)
REVERT: A   73 LYS cc_start: 0.8139 (mttm) cc_final: 0.7841 (mttm)
REVERT: A   93 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8300 (mtm180)
REVERT: A  151 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: A  159 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7480 (mmtt)
REVERT: A  162 ASP cc_start: 0.7840 (m-30) cc_final: 0.7602 (m-30)
REVERT: A  185 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7762 (mtm-85)
REVERT: A  244 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7565 (mm-30)
REVERT: A  245 LEU cc_start: 0.8318 (mt) cc_final: 0.8045 (mp)
  outliers start: 26
  outliers final: 12
  residues processed: 248
  average time/residue: 0.4818
  time to fit residues: 127.5384
Evaluate side-chains
  243 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 229
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0770
   chunk 85 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 239 ASN
N  77 ASN
A  28 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.131306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.116372 restraints weight = 11660.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.84
r_work: 0.3473 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8643  Z= 0.144
  Angle     :  0.519  11.119  11726  Z= 0.270
  Chirality :  0.042   0.149   1323
  Planarity :  0.004   0.057   1492
  Dihedral  :  4.121  26.877   1177
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.92 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.27), residues: 1061
  helix:  2.04 (0.26), residues: 424
  sheet: -0.56 (0.32), residues: 236
  loop : -0.59 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 169 
 TYR   0.009   0.001   TYR R 100 
 PHE   0.012   0.001   PHE N  68 
 TRP   0.016   0.001   TRP A  96 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8638)
  covalent geometry    : angle       0.51866 (11716)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       1.00160 (   10)
  hydrogen bonds       : bond        0.03623 (  424)
  hydrogen bonds       : angle       4.59266 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 232
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   39 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8229 (mp)
REVERT: R  106 LEU cc_start: 0.7956 (tp) cc_final: 0.7729 (tt)
REVERT: R  187 MET cc_start: 0.7389 (mtp) cc_final: 0.7017 (mtp)
REVERT: R  215 VAL cc_start: 0.8488 (t) cc_final: 0.8152 (m)
REVERT: R  267 LEU cc_start: 0.8061 (mm) cc_final: 0.7788 (mm)
REVERT: R  284 PHE cc_start: 0.8188 (m-80) cc_final: 0.7741 (m-80)
REVERT: B   19 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7693 (ttp-110)
REVERT: B  251 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8206 (mtt90)
REVERT: N   52 SER cc_start: 0.8332 (t) cc_final: 0.8078 (t)
REVERT: A   73 LYS cc_start: 0.8141 (mttm) cc_final: 0.7847 (mttm)
REVERT: A   93 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8267 (mtm180)
REVERT: A  126 LYS cc_start: 0.8299 (ttmm) cc_final: 0.8016 (ttmm)
REVERT: A  149 LEU cc_start: 0.8742 (tm) cc_final: 0.8433 (tp)
REVERT: A  151 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7368 (mm-30)
REVERT: A  159 LYS cc_start: 0.8052 (mmpt) cc_final: 0.7453 (mmpt)
REVERT: A  162 ASP cc_start: 0.7840 (m-30) cc_final: 0.7596 (m-30)
REVERT: A  244 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7616 (mm-30)
  outliers start: 23
  outliers final: 15
  residues processed: 244
  average time/residue: 0.4899
  time to fit residues: 127.6411
Evaluate side-chains
  244 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 227
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  170 SER
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  217 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 88 optimal weight:    0.2980
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.131407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.116580 restraints weight = 11626.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.84
r_work: 0.3476 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8643  Z= 0.138
  Angle     :  0.518  11.108  11726  Z= 0.268
  Chirality :  0.042   0.146   1323
  Planarity :  0.004   0.056   1492
  Dihedral  :  4.099  26.724   1177
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.58 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.27), residues: 1061
  helix:  2.11 (0.26), residues: 424
  sheet: -0.53 (0.32), residues: 234
  loop : -0.62 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A  61 
 TYR   0.009   0.001   TYR R 100 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.016   0.001   TRP A  96 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8638)
  covalent geometry    : angle       0.51733 (11716)
  SS BOND              : bond        0.00155 (    5)
  SS BOND              : angle       0.96355 (   10)
  hydrogen bonds       : bond        0.03504 (  424)
  hydrogen bonds       : angle       4.52177 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 231
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   39 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8226 (mp)
REVERT: R  106 LEU cc_start: 0.7948 (tp) cc_final: 0.7726 (tt)
REVERT: R  187 MET cc_start: 0.7372 (mtp) cc_final: 0.7010 (mtp)
REVERT: R  267 LEU cc_start: 0.8055 (mm) cc_final: 0.7770 (mm)
REVERT: R  284 PHE cc_start: 0.8221 (m-80) cc_final: 0.7696 (m-80)
REVERT: B   19 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7665 (ttp-110)
REVERT: B  228 ASP cc_start: 0.7491 (m-30) cc_final: 0.7218 (m-30)
REVERT: B  251 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8216 (mtt90)
REVERT: N   52 SER cc_start: 0.8321 (t) cc_final: 0.8060 (t)
REVERT: A   73 LYS cc_start: 0.8126 (mttm) cc_final: 0.7838 (mttm)
REVERT: A   93 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8298 (mtm180)
REVERT: A  124 ASP cc_start: 0.8017 (m-30) cc_final: 0.7622 (m-30)
REVERT: A  149 LEU cc_start: 0.8753 (tm) cc_final: 0.8454 (tp)
REVERT: A  151 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A  159 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7433 (mmpt)
REVERT: A  162 ASP cc_start: 0.7818 (m-30) cc_final: 0.7571 (m-30)
REVERT: A  185 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7798 (mtm-85)
REVERT: A  244 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7634 (mm-30)
  outliers start: 29
  outliers final: 19
  residues processed: 245
  average time/residue: 0.4869
  time to fit residues: 127.4998
Evaluate side-chains
  252 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 230
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  170 SER
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  217 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 96 optimal weight:    0.0070
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 239 ASN
N  77 ASN
A  28 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.130247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.115423 restraints weight = 11547.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.83
r_work: 0.3477 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8643  Z= 0.139
  Angle     :  0.519  11.226  11726  Z= 0.269
  Chirality :  0.042   0.142   1323
  Planarity :  0.004   0.056   1492
  Dihedral  :  4.080  26.607   1177
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.78 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.27), residues: 1061
  helix:  2.17 (0.26), residues: 424
  sheet: -0.58 (0.32), residues: 236
  loop : -0.55 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  61 
 TYR   0.009   0.001   TYR R 163 
 PHE   0.010   0.001   PHE R 114 
 TRP   0.016   0.001   TRP A  96 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8638)
  covalent geometry    : angle       0.51857 (11716)
  SS BOND              : bond        0.00167 (    5)
  SS BOND              : angle       0.94752 (   10)
  hydrogen bonds       : bond        0.03444 (  424)
  hydrogen bonds       : angle       4.50446 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  106 LEU cc_start: 0.7936 (tp) cc_final: 0.7723 (tt)
REVERT: R  187 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6961 (mtp)
REVERT: R  267 LEU cc_start: 0.8065 (mm) cc_final: 0.7772 (mm)
REVERT: R  284 PHE cc_start: 0.8244 (m-80) cc_final: 0.7700 (m-80)
REVERT: B   19 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7667 (ttp-110)
REVERT: B   76 ASP cc_start: 0.7528 (p0) cc_final: 0.7309 (p0)
REVERT: B  228 ASP cc_start: 0.7373 (m-30) cc_final: 0.7104 (m-30)
REVERT: B  251 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8221 (mtt90)
REVERT: N   52 SER cc_start: 0.8311 (t) cc_final: 0.8048 (t)
REVERT: A   73 LYS cc_start: 0.8118 (mttm) cc_final: 0.7851 (mttm)
REVERT: A   93 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8294 (mtm180)
REVERT: A  124 ASP cc_start: 0.7996 (m-30) cc_final: 0.7608 (m-30)
REVERT: A  149 LEU cc_start: 0.8753 (tm) cc_final: 0.8461 (tp)
REVERT: A  151 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7432 (mm-30)
REVERT: A  159 LYS cc_start: 0.8008 (mmpt) cc_final: 0.7417 (mmtt)
REVERT: A  162 ASP cc_start: 0.7812 (m-30) cc_final: 0.7554 (m-30)
REVERT: A  244 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7639 (mm-30)
  outliers start: 25
  outliers final: 15
  residues processed: 244
  average time/residue: 0.4777
  time to fit residues: 124.5913
Evaluate side-chains
  244 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 226
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0010
   chunk 17 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.131902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.117025 restraints weight = 11644.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.85
r_work: 0.3489 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8643  Z= 0.121
  Angle     :  0.515  10.914  11726  Z= 0.265
  Chirality :  0.042   0.137   1323
  Planarity :  0.004   0.055   1492
  Dihedral  :  4.019  26.137   1177
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.21 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.27), residues: 1061
  helix:  2.26 (0.26), residues: 424
  sheet: -0.46 (0.32), residues: 238
  loop : -0.50 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 169 
 TYR   0.008   0.001   TYR A 191 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.016   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8638)
  covalent geometry    : angle       0.51436 (11716)
  SS BOND              : bond        0.00135 (    5)
  SS BOND              : angle       0.88307 (   10)
  hydrogen bonds       : bond        0.03319 (  424)
  hydrogen bonds       : angle       4.43091 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 232
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   36 TYR cc_start: 0.7735 (t80) cc_final: 0.7377 (m-80)
REVERT: R   85 VAL cc_start: 0.7801 (m) cc_final: 0.7380 (p)
REVERT: R  106 LEU cc_start: 0.7901 (tp) cc_final: 0.7688 (tt)
REVERT: R  187 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6944 (mtp)
REVERT: R  267 LEU cc_start: 0.8069 (mm) cc_final: 0.7791 (mm)
REVERT: R  284 PHE cc_start: 0.8238 (m-80) cc_final: 0.7686 (m-80)
REVERT: B   19 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7651 (ttp-110)
REVERT: N   52 SER cc_start: 0.8314 (t) cc_final: 0.8048 (t)
REVERT: A   73 LYS cc_start: 0.8087 (mttm) cc_final: 0.7821 (mttm)
REVERT: A   93 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8293 (mtm180)
REVERT: A  124 ASP cc_start: 0.7995 (m-30) cc_final: 0.7608 (m-30)
REVERT: A  131 ASN cc_start: 0.7910 (t0) cc_final: 0.7570 (t0)
REVERT: A  149 LEU cc_start: 0.8743 (tm) cc_final: 0.8457 (tp)
REVERT: A  151 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7415 (mm-30)
REVERT: A  159 LYS cc_start: 0.8011 (mmpt) cc_final: 0.7405 (mmpt)
REVERT: A  162 ASP cc_start: 0.7793 (m-30) cc_final: 0.7537 (m-30)
REVERT: A  244 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7653 (mm-30)
  outliers start: 33
  outliers final: 20
  residues processed: 246
  average time/residue: 0.4875
  time to fit residues: 128.0183
Evaluate side-chains
  251 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 228
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 ILE
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  208 PHE
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  217 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 81 optimal weight:    0.2980
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0370
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 144 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.132473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.117681 restraints weight = 11540.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.84
r_work: 0.3498 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8643  Z= 0.122
  Angle     :  0.522  10.892  11726  Z= 0.270
  Chirality :  0.042   0.139   1323
  Planarity :  0.004   0.055   1492
  Dihedral  :  4.000  25.768   1177
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.86 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.27), residues: 1061
  helix:  2.30 (0.26), residues: 425
  sheet: -0.45 (0.32), residues: 239
  loop : -0.43 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  61 
 TYR   0.008   0.001   TYR A 191 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.016   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8638)
  covalent geometry    : angle       0.52201 (11716)
  SS BOND              : bond        0.00131 (    5)
  SS BOND              : angle       0.86949 (   10)
  hydrogen bonds       : bond        0.03271 (  424)
  hydrogen bonds       : angle       4.39083 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 226
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   36 TYR cc_start: 0.7707 (t80) cc_final: 0.7347 (m-80)
REVERT: R   85 VAL cc_start: 0.7854 (m) cc_final: 0.7457 (p)
REVERT: R  106 LEU cc_start: 0.7875 (tp) cc_final: 0.7670 (tt)
REVERT: R  124 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7855 (pt)
REVERT: R  187 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6979 (mtp)
REVERT: R  267 LEU cc_start: 0.8057 (mm) cc_final: 0.7786 (mm)
REVERT: R  284 PHE cc_start: 0.8237 (m-80) cc_final: 0.7703 (m-80)
REVERT: B   19 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7680 (ttp-110)
REVERT: B  137 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7605 (tpp80)
REVERT: N   52 SER cc_start: 0.8319 (t) cc_final: 0.8044 (t)
REVERT: A   73 LYS cc_start: 0.8100 (mttm) cc_final: 0.7855 (mttm)
REVERT: A   93 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8319 (mtm180)
REVERT: A  124 ASP cc_start: 0.8000 (m-30) cc_final: 0.7611 (m-30)
REVERT: A  149 LEU cc_start: 0.8729 (tm) cc_final: 0.8457 (tp)
REVERT: A  151 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7401 (mm-30)
REVERT: A  159 LYS cc_start: 0.8000 (mmpt) cc_final: 0.7380 (mmtt)
REVERT: A  162 ASP cc_start: 0.7787 (m-30) cc_final: 0.7510 (m-30)
REVERT: A  230 ASP cc_start: 0.7697 (m-30) cc_final: 0.7436 (m-30)
REVERT: A  244 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7655 (mm-30)
  outliers start: 32
  outliers final: 19
  residues processed: 243
  average time/residue: 0.4893
  time to fit residues: 127.0519
Evaluate side-chains
  247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 224
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 ILE
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  217 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0770
   chunk 94 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.130580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.115737 restraints weight = 11583.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.84
r_work: 0.3472 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8643  Z= 0.177
  Angle     :  0.560  11.298  11726  Z= 0.289
  Chirality :  0.043   0.141   1323
  Planarity :  0.005   0.085   1492
  Dihedral  :  4.164  26.461   1177
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.06 %
    Favored  : 78.00 %
  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 are not related in a simple way.
  whole:  0.82 (0.27), residues: 1061
  helix:  2.19 (0.26), residues: 425
  sheet: -0.60 (0.32), residues: 236
  loop : -0.45 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A  61 
 TYR   0.010   0.001   TYR R 100 
 PHE   0.020   0.001   PHE R 114 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8638)
  covalent geometry    : angle       0.55987 (11716)
  SS BOND              : bond        0.00137 (    5)
  SS BOND              : angle       0.95331 (   10)
  hydrogen bonds       : bond        0.03587 (  424)
  hydrogen bonds       : angle       4.49558 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 223
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   36 TYR cc_start: 0.7734 (t80) cc_final: 0.7373 (m-80)
REVERT: R  106 LEU cc_start: 0.7892 (tp) cc_final: 0.7687 (tt)
REVERT: R  187 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7012 (mtp)
REVERT: R  267 LEU cc_start: 0.8088 (mm) cc_final: 0.7813 (mm)
REVERT: R  284 PHE cc_start: 0.8267 (m-80) cc_final: 0.7634 (m-80)
REVERT: B   19 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (ttp-110)
REVERT: N   52 SER cc_start: 0.8317 (t) cc_final: 0.8056 (t)
REVERT: A   73 LYS cc_start: 0.8180 (mttm) cc_final: 0.7926 (mttm)
REVERT: A   93 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8350 (mtm180)
REVERT: A  124 ASP cc_start: 0.8006 (m-30) cc_final: 0.7619 (m-30)
REVERT: A  149 LEU cc_start: 0.8720 (tm) cc_final: 0.8443 (tp)
REVERT: A  151 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7435 (mm-30)
REVERT: A  159 LYS cc_start: 0.8015 (mmpt) cc_final: 0.7400 (mmtt)
REVERT: A  162 ASP cc_start: 0.7737 (m-30) cc_final: 0.7468 (m-30)
  outliers start: 27
  outliers final: 18
  residues processed: 235
  average time/residue: 0.4748
  time to fit residues: 119.5312
Evaluate side-chains
  244 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 223
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  170 SER
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  208 PHE
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  217 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 103 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.129622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.114717 restraints weight = 11584.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.84
r_work: 0.3458 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8643  Z= 0.199
  Angle     :  0.577  11.700  11726  Z= 0.299
  Chirality :  0.045   0.148   1323
  Planarity :  0.004   0.057   1492
  Dihedral  :  4.248  26.822   1177
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.28 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.27), residues: 1061
  helix:  2.10 (0.26), residues: 426
  sheet: -0.62 (0.31), residues: 242
  loop : -0.41 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A  61 
 TYR   0.012   0.001   TYR R 163 
 PHE   0.017   0.001   PHE R 114 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8638)
  covalent geometry    : angle       0.57655 (11716)
  SS BOND              : bond        0.00155 (    5)
  SS BOND              : angle       1.01118 (   10)
  hydrogen bonds       : bond        0.03733 (  424)
  hydrogen bonds       : angle       4.57338 ( 1221)

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

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

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2122 Ramachandran restraints generated.
    1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   36 TYR cc_start: 0.7767 (t80) cc_final: 0.7411 (m-80)
REVERT: R  187 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7045 (mtp)
REVERT: R  267 LEU cc_start: 0.8059 (mm) cc_final: 0.7789 (mm)
REVERT: B   19 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7736 (ttp-110)
REVERT: B  304 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8118 (mtm-85)
REVERT: N   52 SER cc_start: 0.8358 (t) cc_final: 0.8107 (t)
REVERT: A   73 LYS cc_start: 0.8231 (mttm) cc_final: 0.7986 (mttm)
REVERT: A   93 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8343 (mtm180)
REVERT: A  124 ASP cc_start: 0.8018 (m-30) cc_final: 0.7636 (m-30)
REVERT: A  149 LEU cc_start: 0.8741 (tm) cc_final: 0.8470 (tp)
REVERT: A  151 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: A  159 LYS cc_start: 0.8048 (mmpt) cc_final: 0.7454 (mmtt)
REVERT: A  162 ASP cc_start: 0.7733 (m-30) cc_final: 0.7473 (m-30)
  outliers start: 26
  outliers final: 16
  residues processed: 230
  average time/residue: 0.4867
  time to fit residues: 119.6359
Evaluate side-chains
  241 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 222
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  170 SER
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   93 ARG
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 230 ASN
B 239 ASN
N  77 ASN
A  28 ASN
A 130 ASN
A 144 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.131540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.116761 restraints weight = 11557.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.83
r_work: 0.3481 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8643  Z= 0.137
  Angle     :  0.554  11.152  11726  Z= 0.285
  Chirality :  0.043   0.143   1323
  Planarity :  0.005   0.079   1492
  Dihedral  :  4.162  26.395   1177
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.93 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.27), residues: 1061
  helix:  2.23 (0.26), residues: 425
  sheet: -0.57 (0.32), residues: 234
  loop : -0.47 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A  61 
 TYR   0.009   0.001   TYR R 163 
 PHE   0.017   0.001   PHE R 114 
 TRP   0.016   0.002   TRP A  96 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8638)
  covalent geometry    : angle       0.55311 (11716)
  SS BOND              : bond        0.00173 (    5)
  SS BOND              : angle       0.92747 (   10)
  hydrogen bonds       : bond        0.03444 (  424)
  hydrogen bonds       : angle       4.47080 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3410.50 seconds
wall clock time: 58 minutes 47.52 seconds (3527.52 seconds total)