Starting phenix.real_space_refine
on Thu Mar 13 07:26:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6so5_10266/03_2025/6so5_10266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6so5_10266/03_2025/6so5_10266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2025/6so5_10266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2025/6so5_10266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2025/6so5_10266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2025/6so5_10266.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      73      5.16       5
     C    5673      2.51       5
     N    1425      2.21       5
     O    1565      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8737
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2464
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 18, 'TRANS': 294}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2301
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 17, 'TRANS': 274}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1160
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1160
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 835
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "F"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 816
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 3, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4310  SG  CYS B 289      46.170 112.721  80.191  1.00101.14           S
  ATOM   4333  SG  CYS B 292      44.838 111.737  77.378  1.00 91.48           S

  Time building chain proxies: 5.60, per 1000 atoms: 0.64
  Number of scatterers: 8737
  At special positions: 0
  Unit cell: (87.48, 129.6, 106.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      73     16.00
     O    1565      8.00
     N    1425      7.00
     C    5673      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 208 " - pdb=" SG  CYS E 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 208 " - pdb=" SG  CYS F 284 " distance=1.75

  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: 2.40
  Conformation dependent library (CDL) restraints added in 979.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 289 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 292 "


  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 3 sheets defined
      71.4% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 34
      removed outlier: 4.006A  pdb=" N   ILE A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 63
    Processing helix  chain 'A' and resid 77 through 84
      removed outlier: 3.970A  pdb=" N   ASP A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 112
      removed outlier: 4.177A  pdb=" N   LEU A 109 " --> pdb=" O   ILE A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 125 through 139
      removed outlier: 3.517A  pdb=" N   LYS A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 159
      removed outlier: 4.043A  pdb=" N   VAL A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   MET A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 176
      No H-bonds generated for 'chain 'A' and resid 174 through 176'
    Processing helix  chain 'A' and resid 177 through 203
      removed outlier: 3.838A  pdb=" N   THR A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 182 " --> pdb=" O   ASN A 178 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A 192 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ASN A 195 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   GLN A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      Proline residue:  A 199  - end of helix
    Processing helix  chain 'A' and resid 215 through 238
      removed outlier: 4.053A  pdb=" N   ALA A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 3.543A  pdb=" N   ASP A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
    Processing helix  chain 'A' and resid 289 through 310
      removed outlier: 3.558A  pdb=" N   ASP A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 340
      removed outlier: 4.087A  pdb=" N   LYS A 330 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL A 331 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 33
    Processing helix  chain 'B' and resid 49 through 64
    Processing helix  chain 'B' and resid 77 through 84
      removed outlier: 3.586A  pdb=" N   ASP B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 119
      removed outlier: 3.765A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
      Proline residue:  B 115  - end of helix
    Processing helix  chain 'B' and resid 128 through 134
      removed outlier: 4.476A  pdb=" N   GLU B 134 " --> pdb=" O   LYS B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 157
    Processing helix  chain 'B' and resid 175 through 182
      Proline residue:  B 180  - end of helix
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 4.597A  pdb=" N   LEU B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 238
      removed outlier: 3.661A  pdb=" N   THR B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 251 through 268
    Processing helix  chain 'B' and resid 289 through 308
      removed outlier: 3.610A  pdb=" N   ASP B 308 " --> pdb=" O   ASP B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 338
      removed outlier: 4.217A  pdb=" N   VAL B 331 " --> pdb=" O   GLY B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 27
      removed outlier: 3.740A  pdb=" N   ASN C  22 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 61
      removed outlier: 3.519A  pdb=" N   PHE C  31 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   PHE C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   MET C  35 " --> pdb=" O   PHE C  31 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LYS C  41 " --> pdb=" O   ARG C  37 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ASP C  42 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 124
    Processing helix  chain 'C' and resid 150 through 171
      removed outlier: 4.457A  pdb=" N   CYS C 157 " --> pdb=" O   VAL C 153 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   CYS C 162 " --> pdb=" O   TRP C 158 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   HIS C 171 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 28
      removed outlier: 3.999A  pdb=" N   TRP D  11 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LEU D  15 " --> pdb=" O   TRP D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 62
    Processing helix  chain 'D' and resid 64 through 124
      removed outlier: 8.319A  pdb=" N   ALA D  70 " --> pdb=" O   MET D  66 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ARG D  71 " --> pdb=" O   ASP D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 171
    Processing helix  chain 'E' and resid 190 through 208
      removed outlier: 5.063A  pdb=" N   ALA E 205 " --> pdb=" O   LEU E 201 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   PHE E 206 " --> pdb=" O   GLY E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 231
      removed outlier: 3.951A  pdb=" N   THR E 219 " --> pdb=" O   ALA E 215 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY E 226 " --> pdb=" O   LEU E 222 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU E 227 " --> pdb=" O   ALA E 223 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   TYR E 228 " --> pdb=" O   TYR E 224 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 243 through 251
    Processing helix  chain 'E' and resid 253 through 291
      removed outlier: 4.029A  pdb=" N   MET E 261 " --> pdb=" O   ILE E 257 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU E 288 " --> pdb=" O   CYS E 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 192 through 209
      removed outlier: 3.562A  pdb=" N   LEU F 199 " --> pdb=" O   GLY F 195 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   ALA F 205 " --> pdb=" O   LEU F 201 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   PHE F 206 " --> pdb=" O   GLY F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 215 through 229
      removed outlier: 3.568A  pdb=" N   THR F 219 " --> pdb=" O   ALA F 215 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR F 224 " --> pdb=" O   LEU F 220 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 243 through 251
    Processing helix  chain 'F' and resid 252 through 291
      removed outlier: 3.575A  pdb=" N   VAL F 256 " --> pdb=" O   ILE F 252 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE F 257 " --> pdb=" O   PRO F 253 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   ASN F 258 " --> pdb=" O   ALA F 254 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70
      removed outlier: 6.859A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 10.376A  pdb=" N   THR A 242 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 9.508A  pdb=" N   ASN A 274 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   PHE A 244 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   ILE A 276 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   CYS A 246 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93
    Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 70
      removed outlier: 6.227A  pdb=" N   LEU B  69 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY B  43 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   THR B 272 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   ASN B 274 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   CYS B 246 " --> pdb=" O   ASN B 274 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   HIS B 273 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   VAL B 316 " --> pdb=" O   HIS B 273 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   ILE B 275 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)

    566 hydrogen bonds defined for protein.
    1689 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2719
        1.34 -     1.46: 2033
        1.46 -     1.58: 4049
        1.58 -     1.70: 0
        1.70 -     1.82: 117
  Bond restraints: 8918
  Sorted by residual:
  bond pdb=" N   CYS F 208 "
       pdb=" CA  CYS F 208 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.31e-02 5.83e+03 7.41e+00
  bond pdb=" N   LYS F 209 "
       pdb=" CA  LYS F 209 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.70e+00
  bond pdb=" N   TYR F 210 "
       pdb=" CA  TYR F 210 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.28e-02 6.10e+03 5.44e+00
  bond pdb=" CA  LEU B  28 "
       pdb=" C   LEU B  28 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.031 1.72e-02 3.38e+03 3.15e+00
  bond pdb=" C   ASP B  74 "
       pdb=" N   PRO B  75 "
    ideal  model  delta    sigma   weight residual
    1.337  1.322  0.014 9.80e-03 1.04e+04 2.11e+00
  ... (remaining 8913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 11668
        1.98 -     3.96: 306
        3.96 -     5.94: 62
        5.94 -     7.92: 7
        7.92 -     9.89: 2
  Bond angle restraints: 12045
  Sorted by residual:
  angle pdb=" C   LEU E 274 "
        pdb=" N   CYS E 275 "
        pdb=" CA  CYS E 275 "
      ideal   model   delta    sigma   weight residual
     122.38  112.49    9.89 1.81e+00 3.05e-01 2.99e+01
  angle pdb=" N   ILE E 190 "
        pdb=" CA  ILE E 190 "
        pdb=" C   ILE E 190 "
      ideal   model   delta    sigma   weight residual
     111.91  107.69    4.22 8.90e-01 1.26e+00 2.25e+01
  angle pdb=" CA  CYS E 275 "
        pdb=" CB  CYS E 275 "
        pdb=" SG  CYS E 275 "
      ideal   model   delta    sigma   weight residual
     114.40  123.08   -8.68 2.30e+00 1.89e-01 1.42e+01
  angle pdb=" N   CYS F 208 "
        pdb=" CA  CYS F 208 "
        pdb=" C   CYS F 208 "
      ideal   model   delta    sigma   weight residual
     113.18  108.71    4.47 1.21e+00 6.83e-01 1.36e+01
  angle pdb=" N   ALA C   6 "
        pdb=" CA  ALA C   6 "
        pdb=" C   ALA C   6 "
      ideal   model   delta    sigma   weight residual
     111.82  107.62    4.20 1.16e+00 7.43e-01 1.31e+01
  ... (remaining 12040 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4663
       16.21 -    32.42: 596
       32.42 -    48.62: 124
       48.62 -    64.83: 21
       64.83 -    81.04: 8
  Dihedral angle restraints: 5412
    sinusoidal: 2193
      harmonic: 3219
  Sorted by residual:
  dihedral pdb=" CB  CYS F 208 "
           pdb=" SG  CYS F 208 "
           pdb=" SG  CYS F 284 "
           pdb=" CB  CYS F 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.23   69.23     1      1.00e+01 1.00e-02 6.19e+01
  dihedral pdb=" CA  SER F 212 "
           pdb=" C   SER F 212 "
           pdb=" N   ILE F 213 "
           pdb=" CA  ILE F 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.56  -29.44     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  HIS E 285 "
           pdb=" C   HIS E 285 "
           pdb=" N   GLU E 286 "
           pdb=" CA  GLU E 286 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.32   22.68     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 5409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 933
       0.039 -    0.078: 330
       0.078 -    0.117: 104
       0.117 -    0.156: 15
       0.156 -    0.195: 4
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  CYS E 275 "
            pdb=" N   CYS E 275 "
            pdb=" C   CYS E 275 "
            pdb=" CB  CYS E 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.53e-01
  chirality pdb=" CA  PRO D  29 "
            pdb=" N   PRO D  29 "
            pdb=" C   PRO D  29 "
            pdb=" CB  PRO D  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CB  ILE F 252 "
            pdb=" CA  ILE F 252 "
            pdb=" CG1 ILE F 252 "
            pdb=" CG2 ILE F 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.86e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 168 "    0.047 5.00e-02 4.00e+02   7.14e-02 8.17e+00
        pdb=" N   PRO B 169 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 169 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 169 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F 207 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.31e+00
        pdb=" C   VAL F 207 "    0.040 2.00e-02 2.50e+03
        pdb=" O   VAL F 207 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS F 208 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 159 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.16e+00
        pdb=" C   ILE D 159 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE D 159 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU D 160 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1494 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 130
        2.56 -     3.14: 8344
        3.14 -     3.73: 14458
        3.73 -     4.31: 18665
        4.31 -     4.90: 28255
  Nonbonded interactions: 69852
  Sorted by model distance:
  nonbonded pdb=" CG2 THR E 219 "
            pdb=" CE2 TYR E 277 "
     model   vdw
     1.973 3.760
  nonbonded pdb=" OE1 GLU A 259 "
            pdb=" OH  TYR A 310 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OH  TYR A 256 "
            pdb=" NH2 ARG A 260 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OE2 GLU A 251 "
            pdb=" N   SER A 254 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OE2 GLU C  46 "
            pdb=" NE  ARG C  50 "
     model   vdw
     2.223 3.120
  ... (remaining 69847 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 24 through 190 or resid 220 through 344))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'E' and resid 191 through 291)
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.250
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
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   0.046   8918  Z= 0.340
  Angle     :  0.816   9.894  12045  Z= 0.466
  Chirality :  0.044   0.195   1386
  Planarity :  0.005   0.071   1497
  Dihedral  : 14.990  81.038   3308
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 23.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.60 (0.21), residues: 1077
  helix: -2.53 (0.15), residues: 684
  sheet: -4.50 (0.37), residues: 97
  loop : -3.21 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D   9 
 HIS   0.012   0.002   HIS A 296 
 PHE   0.016   0.002   PHE F 283 
 TYR   0.014   0.002   TYR E 224 
 ARG   0.005   0.000   ARG F 204 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ILE cc_start: 0.9192 (mm) cc_final: 0.8870 (tp)
REVERT: A  124 MET cc_start: 0.2545 (ttp) cc_final: 0.2177 (tpp)
REVERT: A  185 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8448 (tpm170)
REVERT: A  189 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7755 (mmm160)
REVERT: A  221 LYS cc_start: 0.9224 (mttt) cc_final: 0.8955 (mmmt)
REVERT: A  241 GLN cc_start: 0.8011 (pt0) cc_final: 0.7765 (pt0)
REVERT: A  257 GLU cc_start: 0.8290 (tp30) cc_final: 0.8023 (tm-30)
REVERT: B  153 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8712 (mmm-85)
REVERT: B  249 ILE cc_start: 0.9427 (mt) cc_final: 0.9149 (tt)
REVERT: B  288 PRO cc_start: 0.7272 (Cg_endo) cc_final: 0.7041 (Cg_exo)
REVERT: C   76 GLU cc_start: 0.8268 (tp30) cc_final: 0.8045 (tp30)
REVERT: C   81 LYS cc_start: 0.9294 (tttt) cc_final: 0.9070 (ttmm)
REVERT: C  155 ILE cc_start: 0.7736 (mt) cc_final: 0.7486 (mt)
REVERT: D   13 LEU cc_start: 0.9003 (tp) cc_final: 0.8549 (tp)
REVERT: D   17 PHE cc_start: 0.8789 (m-80) cc_final: 0.8561 (m-80)
REVERT: D   19 PHE cc_start: 0.8746 (m-80) cc_final: 0.8175 (m-80)
REVERT: D   31 PHE cc_start: 0.6747 (m-80) cc_final: 0.6474 (m-80)
REVERT: D   49 MET cc_start: 0.8686 (mmm) cc_final: 0.8388 (mmm)
REVERT: D   52 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8651 (mt-10)
REVERT: D   53 ILE cc_start: 0.9635 (mt) cc_final: 0.9356 (mt)
REVERT: D   56 MET cc_start: 0.8797 (ptp) cc_final: 0.8494 (mtm)
REVERT: D   57 LYS cc_start: 0.9647 (mttt) cc_final: 0.9290 (mttp)
REVERT: D  101 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9029 (tmtt)
REVERT: D  108 PHE cc_start: 0.8381 (t80) cc_final: 0.8142 (t80)
REVERT: D  123 TYR cc_start: 0.7861 (p90) cc_final: 0.7619 (t80)
REVERT: D  155 ILE cc_start: 0.9369 (mt) cc_final: 0.8812 (mt)
REVERT: E  266 LYS cc_start: 0.8690 (mttt) cc_final: 0.8202 (mtmt)
REVERT: E  273 ASP cc_start: 0.9214 (m-30) cc_final: 0.8807 (m-30)
REVERT: E  274 LEU cc_start: 0.9001 (mm) cc_final: 0.8667 (mm)
REVERT: F  225 MET cc_start: 0.8809 (mmt) cc_final: 0.8543 (mmt)
REVERT: F  227 LEU cc_start: 0.9264 (mt) cc_final: 0.8924 (mm)
REVERT: F  248 LEU cc_start: 0.7080 (pp) cc_final: 0.6838 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 332
  average time/residue: 0.2618
  time to fit residues: 113.1869
Evaluate side-chains
  261 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
B 235 GLN
B 332 ASN
C  45 GLN
C  89 HIS
D  22 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.117055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.084953 restraints weight = 27021.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.087261 restraints weight = 16566.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.088738 restraints weight = 12159.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8918  Z= 0.214
  Angle     :  0.693   8.460  12045  Z= 0.359
  Chirality :  0.045   0.280   1386
  Planarity :  0.005   0.063   1497
  Dihedral  :  5.140  20.391   1162
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  6.19 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.24), residues: 1077
  helix: -0.63 (0.18), residues: 714
  sheet: -3.52 (0.45), residues: 92
  loop : -2.77 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP D 158 
 HIS   0.005   0.001   HIS B 314 
 PHE   0.016   0.002   PHE F 278 
 TYR   0.030   0.002   TYR E 277 
 ARG   0.008   0.001   ARG B 260 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 350
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.8981 (tmm) cc_final: 0.8776 (tmm)
REVERT: A  105 ILE cc_start: 0.9227 (mm) cc_final: 0.8860 (tp)
REVERT: A  131 MET cc_start: 0.6922 (mmt) cc_final: 0.6637 (mmm)
REVERT: A  185 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8479 (tpm170)
REVERT: A  189 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7473 (mmm160)
REVERT: A  221 LYS cc_start: 0.9244 (mttt) cc_final: 0.9044 (mmmt)
REVERT: A  257 GLU cc_start: 0.8456 (tp30) cc_final: 0.8107 (tm-30)
REVERT: A  291 MET cc_start: 0.8565 (mtp) cc_final: 0.8273 (pmm)
REVERT: B   69 LEU cc_start: 0.9064 (tp) cc_final: 0.8852 (tp)
REVERT: B   99 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8321 (t0)
REVERT: B  101 PHE cc_start: 0.8027 (m-10) cc_final: 0.7047 (m-10)
REVERT: B  136 MET cc_start: 0.0844 (mmp) cc_final: 0.0639 (mmm)
REVERT: B  152 MET cc_start: 0.8969 (mmm) cc_final: 0.8627 (mmm)
REVERT: B  153 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8730 (mmm-85)
REVERT: B  241 GLN cc_start: 0.7880 (pt0) cc_final: 0.7646 (pt0)
REVERT: C   49 MET cc_start: 0.8832 (mpp) cc_final: 0.8486 (mmm)
REVERT: C   60 LEU cc_start: 0.9253 (tt) cc_final: 0.8588 (tt)
REVERT: C   68 GLU cc_start: 0.8244 (tp30) cc_final: 0.8004 (tp30)
REVERT: C  157 CYS cc_start: 0.9341 (m) cc_final: 0.9112 (p)
REVERT: D   13 LEU cc_start: 0.8970 (tp) cc_final: 0.8508 (tp)
REVERT: D   17 PHE cc_start: 0.8862 (m-10) cc_final: 0.8578 (m-80)
REVERT: D   47 SER cc_start: 0.9217 (p) cc_final: 0.8904 (p)
REVERT: D   49 MET cc_start: 0.8637 (mmm) cc_final: 0.8205 (mmm)
REVERT: D   55 ASP cc_start: 0.8501 (t70) cc_final: 0.8218 (t70)
REVERT: D   65 MET cc_start: 0.7956 (mtp) cc_final: 0.7740 (mtp)
REVERT: D   72 TYR cc_start: 0.8505 (t80) cc_final: 0.8200 (t80)
REVERT: D  101 LYS cc_start: 0.9271 (tmtt) cc_final: 0.8983 (tmtt)
REVERT: D  163 ASN cc_start: 0.8701 (m110) cc_final: 0.8314 (m110)
REVERT: E  273 ASP cc_start: 0.9246 (m-30) cc_final: 0.8988 (m-30)
REVERT: F  225 MET cc_start: 0.8860 (mmt) cc_final: 0.8656 (mmm)
REVERT: F  227 LEU cc_start: 0.8679 (mt) cc_final: 0.8440 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 353
  average time/residue: 0.2231
  time to fit residues: 104.9935
Evaluate side-chains
  284 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 283
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:   20.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 ASN
** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   8 HIS
D  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.114426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.081762 restraints weight = 27754.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.084135 restraints weight = 16820.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.085664 restraints weight = 12265.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8918  Z= 0.286
  Angle     :  0.720   9.054  12045  Z= 0.377
  Chirality :  0.046   0.246   1386
  Planarity :  0.005   0.053   1497
  Dihedral  :  5.133  18.974   1162
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.95 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.25), residues: 1077
  helix: -0.18 (0.18), residues: 712
  sheet: -3.33 (0.46), residues: 92
  loop : -2.38 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP D 158 
 HIS   0.006   0.001   HIS A 296 
 PHE   0.043   0.002   PHE D  19 
 TYR   0.021   0.002   TYR E 277 
 ARG   0.005   0.000   ARG F 192 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 327
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ILE cc_start: 0.9237 (mm) cc_final: 0.8850 (tp)
REVERT: A  189 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7432 (mmm160)
REVERT: A  221 LYS cc_start: 0.9264 (mttt) cc_final: 0.9053 (mmmt)
REVERT: A  257 GLU cc_start: 0.8567 (tp30) cc_final: 0.8203 (tm-30)
REVERT: A  291 MET cc_start: 0.8649 (mtp) cc_final: 0.8363 (pmm)
REVERT: B   60 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8145 (mm110)
REVERT: B   69 LEU cc_start: 0.9052 (tp) cc_final: 0.8850 (tp)
REVERT: B  101 PHE cc_start: 0.8013 (m-10) cc_final: 0.7532 (m-10)
REVERT: B  152 MET cc_start: 0.9007 (mmm) cc_final: 0.8633 (mmm)
REVERT: B  153 ARG cc_start: 0.9157 (mtt180) cc_final: 0.8767 (mmm-85)
REVERT: B  234 GLU cc_start: 0.9231 (pt0) cc_final: 0.9015 (pt0)
REVERT: B  257 GLU cc_start: 0.8627 (tp30) cc_final: 0.8411 (tp30)
REVERT: C   72 TYR cc_start: 0.8664 (t80) cc_final: 0.8171 (t80)
REVERT: C   82 MET cc_start: 0.9015 (mpp) cc_final: 0.8785 (mpp)
REVERT: C  157 CYS cc_start: 0.9352 (m) cc_final: 0.9104 (p)
REVERT: D   13 LEU cc_start: 0.8994 (tp) cc_final: 0.8515 (tp)
REVERT: D   14 VAL cc_start: 0.9011 (m) cc_final: 0.8807 (m)
REVERT: D   17 PHE cc_start: 0.8850 (m-10) cc_final: 0.8552 (m-80)
REVERT: D   19 PHE cc_start: 0.8757 (m-80) cc_final: 0.8399 (m-80)
REVERT: D   49 MET cc_start: 0.8900 (mmm) cc_final: 0.8101 (mmm)
REVERT: D   55 ASP cc_start: 0.8524 (t70) cc_final: 0.8323 (t70)
REVERT: D   68 GLU cc_start: 0.7717 (tp30) cc_final: 0.7191 (tp30)
REVERT: D   72 TYR cc_start: 0.8525 (t80) cc_final: 0.8238 (t80)
REVERT: D   91 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8734 (mttp)
REVERT: D  155 ILE cc_start: 0.9389 (mt) cc_final: 0.8956 (mt)
REVERT: D  163 ASN cc_start: 0.8754 (m110) cc_final: 0.8198 (m110)
REVERT: E  273 ASP cc_start: 0.9410 (m-30) cc_final: 0.9115 (m-30)
REVERT: E  277 TYR cc_start: 0.8478 (m-80) cc_final: 0.8151 (m-80)
REVERT: F  221 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8669 (tp-100)
REVERT: F  225 MET cc_start: 0.9063 (mmt) cc_final: 0.8404 (mmm)
REVERT: F  227 LEU cc_start: 0.8835 (mt) cc_final: 0.8434 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 328
  average time/residue: 0.2084
  time to fit residues: 92.5483
Evaluate side-chains
  272 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 HIS
C  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.113659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.081741 restraints weight = 28381.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.084016 restraints weight = 17289.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.085495 restraints weight = 12653.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8918  Z= 0.307
  Angle     :  0.724   9.302  12045  Z= 0.380
  Chirality :  0.046   0.243   1386
  Planarity :  0.006   0.061   1497
  Dihedral  :  5.115  19.360   1162
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.95 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.25), residues: 1077
  helix: -0.10 (0.18), residues: 702
  sheet: -3.40 (0.46), residues: 95
  loop : -2.08 (0.41), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP D 158 
 HIS   0.005   0.001   HIS D   8 
 PHE   0.030   0.002   PHE D  19 
 TYR   0.018   0.002   TYR A 148 
 ARG   0.007   0.001   ARG D  93 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 316
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.9087 (tmm) cc_final: 0.8689 (tmm)
REVERT: A  105 ILE cc_start: 0.9224 (mm) cc_final: 0.8922 (tp)
REVERT: A  148 TYR cc_start: 0.8680 (t80) cc_final: 0.8349 (t80)
REVERT: A  221 LYS cc_start: 0.9305 (mttt) cc_final: 0.9071 (mmmt)
REVERT: A  257 GLU cc_start: 0.8584 (tp30) cc_final: 0.8266 (tm-30)
REVERT: A  291 MET cc_start: 0.8629 (mtp) cc_final: 0.8288 (pmm)
REVERT: B   60 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8124 (mm110)
REVERT: B  101 PHE cc_start: 0.8038 (m-10) cc_final: 0.7421 (m-10)
REVERT: B  152 MET cc_start: 0.9021 (mmm) cc_final: 0.8660 (mmm)
REVERT: B  234 GLU cc_start: 0.9232 (pt0) cc_final: 0.9023 (pt0)
REVERT: B  241 GLN cc_start: 0.8044 (pt0) cc_final: 0.7655 (pt0)
REVERT: B  315 ILE cc_start: 0.8857 (mp) cc_final: 0.8621 (mp)
REVERT: C   48 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8706 (tm-30)
REVERT: C   82 MET cc_start: 0.9002 (mpp) cc_final: 0.8508 (mpp)
REVERT: D   17 PHE cc_start: 0.8838 (m-10) cc_final: 0.8623 (m-80)
REVERT: D   19 PHE cc_start: 0.8737 (m-80) cc_final: 0.8464 (m-80)
REVERT: D   49 MET cc_start: 0.8791 (mmm) cc_final: 0.8160 (mmm)
REVERT: D   68 GLU cc_start: 0.7749 (tp30) cc_final: 0.7548 (tp30)
REVERT: D   91 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8875 (mtpp)
REVERT: D  155 ILE cc_start: 0.9486 (mt) cc_final: 0.9228 (mt)
REVERT: D  163 ASN cc_start: 0.8833 (m110) cc_final: 0.8299 (m110)
REVERT: E  204 ARG cc_start: 0.8700 (ppt170) cc_final: 0.8441 (ppt170)
REVERT: E  266 LYS cc_start: 0.8541 (mttt) cc_final: 0.8183 (mtmt)
REVERT: E  273 ASP cc_start: 0.9424 (m-30) cc_final: 0.9121 (m-30)
REVERT: E  277 TYR cc_start: 0.8557 (m-80) cc_final: 0.8078 (m-80)
REVERT: F  221 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8539 (tp-100)
REVERT: F  225 MET cc_start: 0.9063 (mmt) cc_final: 0.8383 (mmm)
REVERT: F  227 LEU cc_start: 0.8789 (mt) cc_final: 0.8425 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 316
  average time/residue: 0.2184
  time to fit residues: 93.6069
Evaluate side-chains
  258 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
B 274 ASN
D  45 GLN
F 285 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.115523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.082970 restraints weight = 28287.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.085511 restraints weight = 16810.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087128 restraints weight = 12125.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8918  Z= 0.243
  Angle     :  0.699   9.550  12045  Z= 0.364
  Chirality :  0.045   0.310   1386
  Planarity :  0.005   0.065   1497
  Dihedral  :  5.048  18.782   1162
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.26), residues: 1077
  helix:  0.12 (0.18), residues: 717
  sheet: -3.04 (0.49), residues: 92
  loop : -2.20 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.002   TRP D 158 
 HIS   0.008   0.001   HIS A 296 
 PHE   0.026   0.002   PHE A 165 
 TYR   0.016   0.001   TYR A 148 
 ARG   0.007   0.001   ARG B 260 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 308
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ILE cc_start: 0.9211 (mm) cc_final: 0.8942 (tp)
REVERT: A  257 GLU cc_start: 0.8545 (tp30) cc_final: 0.8251 (tm-30)
REVERT: A  291 MET cc_start: 0.8602 (mtp) cc_final: 0.8395 (pmm)
REVERT: B   60 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8153 (mm110)
REVERT: B   69 LEU cc_start: 0.9021 (tp) cc_final: 0.8763 (tp)
REVERT: B  152 MET cc_start: 0.9040 (mmm) cc_final: 0.8676 (mmm)
REVERT: B  162 VAL cc_start: 0.8790 (t) cc_final: 0.8535 (m)
REVERT: B  234 GLU cc_start: 0.9235 (pt0) cc_final: 0.9001 (pt0)
REVERT: B  241 GLN cc_start: 0.8054 (pt0) cc_final: 0.7650 (pt0)
REVERT: B  257 GLU cc_start: 0.8552 (tp30) cc_final: 0.8335 (tp30)
REVERT: C   48 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8718 (tm-30)
REVERT: C   49 MET cc_start: 0.9529 (ttp) cc_final: 0.9195 (ttt)
REVERT: C   58 GLN cc_start: 0.8795 (pp30) cc_final: 0.8158 (tm-30)
REVERT: C   59 GLU cc_start: 0.9139 (tp30) cc_final: 0.8931 (tp30)
REVERT: C   60 LEU cc_start: 0.9366 (tt) cc_final: 0.9125 (tp)
REVERT: C   82 MET cc_start: 0.9041 (mpp) cc_final: 0.8673 (mpp)
REVERT: C  159 ILE cc_start: 0.9401 (pt) cc_final: 0.9188 (pt)
REVERT: D   17 PHE cc_start: 0.8856 (m-10) cc_final: 0.8620 (m-80)
REVERT: D   19 PHE cc_start: 0.8774 (m-80) cc_final: 0.8450 (m-80)
REVERT: D   49 MET cc_start: 0.8926 (mmm) cc_final: 0.8136 (mmm)
REVERT: D   55 ASP cc_start: 0.8750 (t70) cc_final: 0.8453 (t70)
REVERT: D   91 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8855 (mtpp)
REVERT: D  155 ILE cc_start: 0.9441 (mt) cc_final: 0.9209 (mt)
REVERT: D  163 ASN cc_start: 0.8769 (m110) cc_final: 0.8213 (m110)
REVERT: E  273 ASP cc_start: 0.9434 (m-30) cc_final: 0.9107 (m-30)
REVERT: E  277 TYR cc_start: 0.8548 (m-80) cc_final: 0.8079 (m-80)
REVERT: F  221 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8503 (tp-100)
REVERT: F  225 MET cc_start: 0.9048 (mmt) cc_final: 0.8489 (mmm)
REVERT: F  227 LEU cc_start: 0.8821 (mt) cc_final: 0.8504 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2087
  time to fit residues: 87.7148
Evaluate side-chains
  260 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 78 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
B 274 ASN
D  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.114524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082277 restraints weight = 28280.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.084736 restraints weight = 17051.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.086302 restraints weight = 12346.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8918  Z= 0.271
  Angle     :  0.720   9.322  12045  Z= 0.375
  Chirality :  0.046   0.307   1386
  Planarity :  0.005   0.068   1497
  Dihedral  :  5.002  18.343   1162
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.48 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.26), residues: 1077
  helix:  0.28 (0.19), residues: 705
  sheet: -3.23 (0.47), residues: 95
  loop : -1.91 (0.41), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.075   0.002   TRP D 158 
 HIS   0.007   0.001   HIS A 296 
 PHE   0.019   0.002   PHE D  19 
 TYR   0.013   0.002   TYR F 277 
 ARG   0.006   0.000   ARG B 260 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 306
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.8950 (tmm) cc_final: 0.8256 (tmm)
REVERT: A  105 ILE cc_start: 0.9215 (mm) cc_final: 0.8997 (tp)
REVERT: A  185 ARG cc_start: 0.8470 (tpm170) cc_final: 0.8254 (tpm170)
REVERT: A  257 GLU cc_start: 0.8523 (tp30) cc_final: 0.8182 (tm-30)
REVERT: B   69 LEU cc_start: 0.8931 (tp) cc_final: 0.8724 (tp)
REVERT: B  152 MET cc_start: 0.9033 (mmm) cc_final: 0.8733 (mmm)
REVERT: B  162 VAL cc_start: 0.8734 (t) cc_final: 0.8481 (m)
REVERT: B  234 GLU cc_start: 0.9216 (pt0) cc_final: 0.8977 (pt0)
REVERT: B  241 GLN cc_start: 0.8056 (pt0) cc_final: 0.7692 (pt0)
REVERT: B  257 GLU cc_start: 0.8528 (tp30) cc_final: 0.8305 (tp30)
REVERT: B  293 GLU cc_start: 0.8573 (pp20) cc_final: 0.8145 (tm-30)
REVERT: C   48 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8830 (tm-30)
REVERT: C   49 MET cc_start: 0.9535 (ttp) cc_final: 0.9261 (ttt)
REVERT: C   58 GLN cc_start: 0.8809 (pp30) cc_final: 0.8211 (tm-30)
REVERT: C   82 MET cc_start: 0.8976 (mpp) cc_final: 0.8663 (mpp)
REVERT: C  157 CYS cc_start: 0.9341 (m) cc_final: 0.9124 (p)
REVERT: D   17 PHE cc_start: 0.8796 (m-10) cc_final: 0.8594 (m-80)
REVERT: D   19 PHE cc_start: 0.8785 (m-80) cc_final: 0.8479 (m-80)
REVERT: D   49 MET cc_start: 0.8912 (mmm) cc_final: 0.8146 (mmm)
REVERT: D   55 ASP cc_start: 0.8681 (t70) cc_final: 0.8282 (t70)
REVERT: D   56 MET cc_start: 0.8874 (ptm) cc_final: 0.8562 (ptm)
REVERT: D  163 ASN cc_start: 0.8783 (m110) cc_final: 0.8231 (m110)
REVERT: E  273 ASP cc_start: 0.9443 (m-30) cc_final: 0.9204 (m-30)
REVERT: E  277 TYR cc_start: 0.8631 (m-80) cc_final: 0.8261 (m-80)
REVERT: F  221 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8382 (tp-100)
REVERT: F  225 MET cc_start: 0.9065 (mmt) cc_final: 0.8267 (mmm)
REVERT: F  229 LYS cc_start: 0.8574 (mppt) cc_final: 0.8362 (tptt)
  outliers start: 1
  outliers final: 1
  residues processed: 307
  average time/residue: 0.2722
  time to fit residues: 114.8747
Evaluate side-chains
  254 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 253
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 42 optimal weight:    0.1980
   chunk 62 optimal weight:    0.0040
   chunk 95 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0050
   chunk 91 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.4206

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS
A 235 GLN
A 274 ASN
B 159 ASN
B 274 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.119765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.087505 restraints weight = 27688.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.090025 restraints weight = 17037.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.091638 restraints weight = 12462.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8918  Z= 0.192
  Angle     :  0.697   9.912  12045  Z= 0.354
  Chirality :  0.046   0.326   1386
  Planarity :  0.005   0.071   1497
  Dihedral  :  4.775  19.360   1162
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1077
  helix:  0.64 (0.19), residues: 709
  sheet: -2.76 (0.50), residues: 91
  loop : -1.96 (0.41), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.084   0.002   TRP D 158 
 HIS   0.006   0.001   HIS F 285 
 PHE   0.035   0.002   PHE A 139 
 TYR   0.012   0.001   TYR E 277 
 ARG   0.008   0.001   ARG B 260 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 325
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.8852 (tmm) cc_final: 0.7821 (tmm)
REVERT: A  136 MET cc_start: 0.4230 (ppp) cc_final: 0.3622 (mpp)
REVERT: A  189 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7773 (mmm160)
REVERT: A  257 GLU cc_start: 0.8360 (tp30) cc_final: 0.8127 (tm-30)
REVERT: A  326 ARG cc_start: 0.7787 (mmm160) cc_final: 0.7511 (mmm-85)
REVERT: B   60 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7920 (mm110)
REVERT: B  152 MET cc_start: 0.8970 (mmm) cc_final: 0.8601 (mmm)
REVERT: B  234 GLU cc_start: 0.9187 (pt0) cc_final: 0.8985 (pt0)
REVERT: B  241 GLN cc_start: 0.7930 (pt0) cc_final: 0.7392 (pp30)
REVERT: B  257 GLU cc_start: 0.8436 (tp30) cc_final: 0.8167 (tp30)
REVERT: B  293 GLU cc_start: 0.8310 (pp20) cc_final: 0.7997 (tm-30)
REVERT: C   58 GLN cc_start: 0.8679 (pp30) cc_final: 0.8137 (tm-30)
REVERT: C   82 MET cc_start: 0.8897 (mpp) cc_final: 0.8654 (mpp)
REVERT: D   49 MET cc_start: 0.8756 (mmm) cc_final: 0.8299 (mmm)
REVERT: D   55 ASP cc_start: 0.8715 (t70) cc_final: 0.8267 (t70)
REVERT: D   63 VAL cc_start: 0.9172 (t) cc_final: 0.8859 (p)
REVERT: D   72 TYR cc_start: 0.8477 (t80) cc_final: 0.8153 (t80)
REVERT: D   91 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8753 (mttp)
REVERT: E  273 ASP cc_start: 0.9407 (m-30) cc_final: 0.9024 (m-30)
REVERT: E  277 TYR cc_start: 0.8466 (m-80) cc_final: 0.8120 (m-80)
REVERT: F  221 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8254 (tp-100)
REVERT: F  225 MET cc_start: 0.8987 (mmt) cc_final: 0.8229 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 325
  average time/residue: 0.2174
  time to fit residues: 96.6012
Evaluate side-chains
  263 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0870
   chunk 51 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 95 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
D  22 ASN
D  45 GLN
D  54 GLN
D 112 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.119342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.086840 restraints weight = 27949.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.089315 restraints weight = 17385.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.090914 restraints weight = 12818.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8918  Z= 0.211
  Angle     :  0.718  10.687  12045  Z= 0.370
  Chirality :  0.046   0.318   1386
  Planarity :  0.005   0.064   1497
  Dihedral  :  4.613  17.226   1162
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.34 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.26), residues: 1077
  helix:  0.70 (0.19), residues: 709
  sheet: -2.68 (0.51), residues: 92
  loop : -2.06 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.091   0.002   TRP D 158 
 HIS   0.005   0.001   HIS A 172 
 PHE   0.031   0.002   PHE E 278 
 TYR   0.014   0.001   TYR E 277 
 ARG   0.007   0.000   ARG A 326 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 308
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.8877 (tmm) cc_final: 0.7874 (tmm)
REVERT: A  105 ILE cc_start: 0.9211 (tp) cc_final: 0.8973 (tp)
REVERT: A  257 GLU cc_start: 0.8391 (tp30) cc_final: 0.8125 (tm-30)
REVERT: A  326 ARG cc_start: 0.7797 (mmm160) cc_final: 0.7494 (mmm-85)
REVERT: B  152 MET cc_start: 0.8996 (mmm) cc_final: 0.8564 (mmm)
REVERT: B  153 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8571 (ptp-170)
REVERT: B  234 GLU cc_start: 0.9185 (pt0) cc_final: 0.8964 (pt0)
REVERT: B  257 GLU cc_start: 0.8457 (tp30) cc_final: 0.8177 (tp30)
REVERT: B  293 GLU cc_start: 0.8325 (pp20) cc_final: 0.7813 (tm-30)
REVERT: C   49 MET cc_start: 0.9393 (ttt) cc_final: 0.9182 (ttm)
REVERT: C   58 GLN cc_start: 0.8730 (pp30) cc_final: 0.8189 (tm-30)
REVERT: C   66 MET cc_start: 0.8280 (tpp) cc_final: 0.7586 (tpt)
REVERT: C   82 MET cc_start: 0.8927 (mpp) cc_final: 0.8651 (mpp)
REVERT: D   17 PHE cc_start: 0.8706 (m-80) cc_final: 0.8245 (m-80)
REVERT: D   49 MET cc_start: 0.8830 (mmm) cc_final: 0.8407 (mmm)
REVERT: D   52 GLU cc_start: 0.8913 (tp30) cc_final: 0.8700 (tp30)
REVERT: D   63 VAL cc_start: 0.9136 (t) cc_final: 0.8795 (p)
REVERT: D   72 TYR cc_start: 0.8219 (t80) cc_final: 0.7579 (t80)
REVERT: D   76 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8601 (mm-30)
REVERT: D   91 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8722 (mttp)
REVERT: D  163 ASN cc_start: 0.8408 (m110) cc_final: 0.8018 (m110)
REVERT: E  273 ASP cc_start: 0.9422 (m-30) cc_final: 0.9036 (m-30)
REVERT: E  277 TYR cc_start: 0.8489 (m-80) cc_final: 0.8118 (m-80)
REVERT: F  221 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8159 (tp-100)
REVERT: F  225 MET cc_start: 0.8932 (mmt) cc_final: 0.8180 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 310
  average time/residue: 0.2028
  time to fit residues: 85.8129
Evaluate side-chains
  252 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 64 optimal weight:    0.6980
   chunk 92 optimal weight:    0.0470
   chunk 72 optimal weight:    0.0870
   chunk 51 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
A 296 HIS
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  45 GLN
D  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.120272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.087210 restraints weight = 27769.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.089912 restraints weight = 16807.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.091665 restraints weight = 12146.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.5478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8918  Z= 0.212
  Angle     :  0.749  10.300  12045  Z= 0.384
  Chirality :  0.046   0.327   1386
  Planarity :  0.005   0.061   1497
  Dihedral  :  4.686  18.734   1162
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.62 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.26), residues: 1077
  helix:  0.74 (0.19), residues: 700
  sheet: -2.44 (0.51), residues: 90
  loop : -1.95 (0.40), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.096   0.002   TRP D 158 
 HIS   0.004   0.001   HIS E 285 
 PHE   0.036   0.002   PHE E 278 
 TYR   0.012   0.001   TYR E 277 
 ARG   0.005   0.000   ARG A 326 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 314
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9064 (mtpp)
REVERT: A  185 ARG cc_start: 0.8382 (tpm170) cc_final: 0.8137 (tpt90)
REVERT: A  189 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7856 (mmm160)
REVERT: A  257 GLU cc_start: 0.8386 (tp30) cc_final: 0.8122 (tm-30)
REVERT: A  326 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7478 (mmm-85)
REVERT: B  152 MET cc_start: 0.8975 (mmm) cc_final: 0.8559 (mmm)
REVERT: B  153 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8613 (ptp-170)
REVERT: B  235 GLN cc_start: 0.9033 (mt0) cc_final: 0.8533 (mt0)
REVERT: B  257 GLU cc_start: 0.8520 (tp30) cc_final: 0.8243 (tp30)
REVERT: B  293 GLU cc_start: 0.8349 (pp20) cc_final: 0.7851 (tm-30)
REVERT: C   58 GLN cc_start: 0.8737 (pp30) cc_final: 0.8320 (tm-30)
REVERT: C   71 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8725 (ttp80)
REVERT: C   79 ILE cc_start: 0.9535 (mm) cc_final: 0.9265 (mm)
REVERT: C   82 MET cc_start: 0.8879 (mpp) cc_final: 0.8586 (mpp)
REVERT: D    9 TRP cc_start: 0.5013 (m-10) cc_final: 0.4790 (m-10)
REVERT: D   12 LEU cc_start: 0.8938 (mt) cc_final: 0.8467 (pp)
REVERT: D   17 PHE cc_start: 0.8588 (m-80) cc_final: 0.8245 (m-80)
REVERT: D   49 MET cc_start: 0.8777 (mmm) cc_final: 0.8501 (mmm)
REVERT: D   52 GLU cc_start: 0.8862 (tp30) cc_final: 0.8550 (tp30)
REVERT: D   56 MET cc_start: 0.8955 (ptm) cc_final: 0.8723 (ptt)
REVERT: D   63 VAL cc_start: 0.9034 (t) cc_final: 0.8771 (p)
REVERT: D   91 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8758 (mttp)
REVERT: D  163 ASN cc_start: 0.8322 (m110) cc_final: 0.7985 (m110)
REVERT: E  204 ARG cc_start: 0.8432 (ppt170) cc_final: 0.8124 (ppt170)
REVERT: E  269 GLU cc_start: 0.9270 (pt0) cc_final: 0.9035 (mm-30)
REVERT: E  273 ASP cc_start: 0.9432 (m-30) cc_final: 0.8993 (m-30)
REVERT: E  277 TYR cc_start: 0.8528 (m-80) cc_final: 0.8152 (m-80)
REVERT: F  221 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8093 (tp-100)
REVERT: F  225 MET cc_start: 0.8960 (mmt) cc_final: 0.8213 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 315
  average time/residue: 0.1993
  time to fit residues: 85.6778
Evaluate side-chains
  263 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 90 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 106 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 99 optimal weight:   50.0000
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 296 HIS
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
D  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.119456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.086313 restraints weight = 27764.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.088925 restraints weight = 16716.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.090633 restraints weight = 12050.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.5575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8918  Z= 0.230
  Angle     :  0.774  10.373  12045  Z= 0.397
  Chirality :  0.047   0.321   1386
  Planarity :  0.005   0.060   1497
  Dihedral  :  4.654  19.820   1162
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.41 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.26), residues: 1077
  helix:  0.68 (0.19), residues: 694
  sheet: -2.42 (0.52), residues: 89
  loop : -1.77 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.100   0.003   TRP D 158 
 HIS   0.015   0.002   HIS C  89 
 PHE   0.037   0.002   PHE E 278 
 TYR   0.012   0.001   TYR E 277 
 ARG   0.005   0.000   ARG A 326 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 303
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9074 (mtpp)
REVERT: A  105 ILE cc_start: 0.9279 (tp) cc_final: 0.9069 (tp)
REVERT: A  257 GLU cc_start: 0.8425 (tp30) cc_final: 0.8148 (tm-30)
REVERT: A  326 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7553 (mmm-85)
REVERT: B  152 MET cc_start: 0.8975 (mmm) cc_final: 0.8531 (mmm)
REVERT: B  153 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8623 (ptp-170)
REVERT: B  241 GLN cc_start: 0.6669 (pp30) cc_final: 0.6174 (pp30)
REVERT: B  257 GLU cc_start: 0.8508 (tp30) cc_final: 0.8213 (tp30)
REVERT: B  293 GLU cc_start: 0.8364 (pp20) cc_final: 0.7874 (tm-30)
REVERT: B  295 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8320 (mmm160)
REVERT: C   58 GLN cc_start: 0.8813 (pp30) cc_final: 0.8273 (tm-30)
REVERT: C   68 GLU cc_start: 0.8473 (tp30) cc_final: 0.8184 (tp30)
REVERT: C   71 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8740 (ttp80)
REVERT: C   82 MET cc_start: 0.8929 (mpp) cc_final: 0.8607 (mpp)
REVERT: D    9 TRP cc_start: 0.5052 (m-10) cc_final: 0.4812 (m-10)
REVERT: D   12 LEU cc_start: 0.8952 (mt) cc_final: 0.8493 (pp)
REVERT: D   17 PHE cc_start: 0.8586 (m-80) cc_final: 0.8225 (m-80)
REVERT: D   49 MET cc_start: 0.8740 (mmm) cc_final: 0.8496 (mmm)
REVERT: D   52 GLU cc_start: 0.8886 (tp30) cc_final: 0.8255 (tp30)
REVERT: D   55 ASP cc_start: 0.8720 (t70) cc_final: 0.8301 (t70)
REVERT: D   59 GLU cc_start: 0.8811 (pt0) cc_final: 0.8356 (pt0)
REVERT: D   91 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8770 (mttp)
REVERT: D  163 ASN cc_start: 0.8327 (m110) cc_final: 0.8006 (m110)
REVERT: E  266 LYS cc_start: 0.8599 (mttt) cc_final: 0.8279 (mtmt)
REVERT: E  273 ASP cc_start: 0.9456 (m-30) cc_final: 0.9014 (m-30)
REVERT: E  277 TYR cc_start: 0.8542 (m-80) cc_final: 0.8201 (m-80)
REVERT: F  221 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8140 (tp-100)
REVERT: F  225 MET cc_start: 0.8990 (mmt) cc_final: 0.8214 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 304
  average time/residue: 0.2037
  time to fit residues: 84.6910
Evaluate side-chains
  256 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 255
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
D  54 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.119710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.086647 restraints weight = 27933.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.089334 restraints weight = 16704.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.091099 restraints weight = 11999.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.5631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8918  Z= 0.227
  Angle     :  0.768   9.723  12045  Z= 0.395
  Chirality :  0.047   0.322   1386
  Planarity :  0.005   0.059   1497
  Dihedral  :  4.682  20.351   1162
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.26), residues: 1077
  helix:  0.59 (0.19), residues: 709
  sheet: -2.50 (0.51), residues: 90
  loop : -1.98 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.100   0.003   TRP D 158 
 HIS   0.010   0.001   HIS C  89 
 PHE   0.038   0.002   PHE E 278 
 TYR   0.018   0.002   TYR C  72 
 ARG   0.005   0.000   ARG A 326 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3495.71 seconds
wall clock time: 62 minutes 19.18 seconds (3739.18 seconds total)