Starting phenix.real_space_refine
on Tue Mar  3 20:55:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ezh_31387/03_2026/7ezh_31387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ezh_31387/03_2026/7ezh_31387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ezh_31387/03_2026/7ezh_31387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ezh_31387/03_2026/7ezh_31387.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ezh_31387/03_2026/7ezh_31387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ezh_31387/03_2026/7ezh_31387.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    5643      2.51       5
     N    1489      2.21       5
     O    1634      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8838
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1753
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2561
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2306
          Classifications: {'peptide': 296}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 12, 'TRANS': 283}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "G"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 404
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "H"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1736
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYS:plan-2': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 2.20, per 1000 atoms: 0.25
  Number of scatterers: 8838
  At special positions: 0
  Unit cell: (106.59, 112.86, 119.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    1634      8.00
     N    1489      7.00
     C    5643      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 114 " - pdb=" SG  CYS D 196 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 381.2 milliseconds
  

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 13 sheets defined
      41.1% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.509A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 53
      removed outlier: 3.995A  pdb=" N   LYS A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.053A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.928A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.513A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 5.355A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.657A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 69
    Processing helix  chain 'D' and resid 70 through 73
    Processing helix  chain 'D' and resid 74 through 105
      Proline residue:  D  96  - end of helix
      Proline residue:  D 101  - end of helix
    Processing helix  chain 'D' and resid 110 through 145
    Processing helix  chain 'D' and resid 145 through 153
      removed outlier: 3.589A  pdb=" N   ARG D 150 " --> pdb=" O   PRO D 146 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL D 151 " --> pdb=" O   LEU D 147 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP D 152 " --> pdb=" O   GLN D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 173
    Processing helix  chain 'D' and resid 174 through 179
    Processing helix  chain 'D' and resid 202 through 218
    Processing helix  chain 'D' and resid 218 through 245
      removed outlier: 3.693A  pdb=" N   GLY D 239 " --> pdb=" O   GLU D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 339
      removed outlier: 3.508A  pdb=" N   LYS D 308 " --> pdb=" O   ASN D 304 " (cutoff:3.500A)
      Proline residue:  D 328  - end of helix
    Processing helix  chain 'D' and resid 339 through 348
    Processing helix  chain 'D' and resid 349 through 370
      removed outlier: 3.719A  pdb=" N   SER D 362 " --> pdb=" O   LEU D 358 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER D 363 " --> pdb=" O   SER D 359 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS D 364 " --> pdb=" O   TYR D 360 " (cutoff:3.500A)
      Proline residue:  D 367  - end of helix
    Processing helix  chain 'D' and resid 371 through 373
      No H-bonds generated for 'chain 'D' and resid 371 through 373'
    Processing helix  chain 'D' and resid 374 through 384
      removed outlier: 4.364A  pdb=" N   MET D 382 " --> pdb=" O   ARG D 378 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 25
      removed outlier: 3.662A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.658A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.926A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.570A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.867A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.483A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.722A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.771A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.801A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 180 through 187
      removed outlier: 3.609A  pdb=" N   ARG D 197 " --> pdb=" O   ASN D 181 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN D 191 " --> pdb=" O   LYS D 187 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.561A  pdb=" N   ALA H  92 " --> pdb=" O   LEU H 117 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142
      removed outlier: 3.730A  pdb=" N   CYS H 159 " --> pdb=" O   PHE H 212 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE H 212 " --> pdb=" O   CYS H 159 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.760A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1317 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.48

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2822
        1.35 -     1.47: 2251
        1.47 -     1.59: 3841
        1.59 -     1.71: 1
        1.71 -     1.83: 107
  Bond restraints: 9022
  Sorted by residual:
  bond pdb=" O1  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.462  1.635 -0.173 2.00e-02 2.50e+03 7.45e+01
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.537  0.142 2.00e-02 2.50e+03 5.07e+01
  bond pdb=" N   VAL H 119 "
       pdb=" CA  VAL H 119 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.15e-02 7.56e+03 1.42e+01
  bond pdb=" N   SER H 120 "
       pdb=" CA  SER H 120 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.29e-02 6.01e+03 5.13e+00
  bond pdb=" N   ASP A 350 "
       pdb=" CA  ASP A 350 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.46e+00
  ... (remaining 9017 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 11975
        1.93 -     3.85: 225
        3.85 -     5.78: 26
        5.78 -     7.71: 9
        7.71 -     9.63: 3
  Bond angle restraints: 12238
  Sorted by residual:
  angle pdb=" N   SER A 326 "
        pdb=" CA  SER A 326 "
        pdb=" C   SER A 326 "
      ideal   model   delta    sigma   weight residual
     111.14  104.94    6.20 1.08e+00 8.57e-01 3.30e+01
  angle pdb=" C   GLN D 153 "
        pdb=" CA  GLN D 153 "
        pdb=" CB  GLN D 153 "
      ideal   model   delta    sigma   weight residual
     111.88  104.45    7.43 1.41e+00 5.03e-01 2.77e+01
  angle pdb=" C   THR A 329 "
        pdb=" CA  THR A 329 "
        pdb=" CB  THR A 329 "
      ideal   model   delta    sigma   weight residual
     110.42  118.59   -8.17 1.99e+00 2.53e-01 1.69e+01
  angle pdb=" CA  ALA H 136 "
        pdb=" C   ALA H 136 "
        pdb=" O   ALA H 136 "
      ideal   model   delta    sigma   weight residual
     121.54  117.25    4.29 1.16e+00 7.43e-01 1.37e+01
  angle pdb=" N   GLY B 141 "
        pdb=" CA  GLY B 141 "
        pdb=" C   GLY B 141 "
      ideal   model   delta    sigma   weight residual
     113.18  121.71   -8.53 2.37e+00 1.78e-01 1.30e+01
  ... (remaining 12233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 4876
       16.62 -    33.23: 384
       33.23 -    49.85: 55
       49.85 -    66.46: 13
       66.46 -    83.08: 8
  Dihedral angle restraints: 5336
    sinusoidal: 2000
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.62  -56.62     1      1.00e+01 1.00e-02 4.32e+01
  dihedral pdb=" CA  LEU D 200 "
           pdb=" C   LEU D 200 "
           pdb=" N   PRO D 201 "
           pdb=" CA  PRO D 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.44  -27.56     0      5.00e+00 4.00e-02 3.04e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.31   26.69     0      5.00e+00 4.00e-02 2.85e+01
  ... (remaining 5333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1296
       0.079 -    0.159: 110
       0.159 -    0.238: 3
       0.238 -    0.317: 0
       0.317 -    0.397: 1
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" CA  THR A 329 "
            pdb=" N   THR A 329 "
            pdb=" C   THR A 329 "
            pdb=" CB  THR A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  GLN D 153 "
            pdb=" N   GLN D 153 "
            pdb=" C   GLN D 153 "
            pdb=" CB  GLN D 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  THR A 327 "
            pdb=" N   THR A 327 "
            pdb=" C   THR A 327 "
            pdb=" CB  THR A 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.17 2.00e-01 2.50e+01 7.47e-01
  ... (remaining 1407 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 214 "   -0.021 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   LEU D 214 "    0.074 2.00e-02 2.50e+03
        pdb=" O   LEU D 214 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   LEU D 215 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 325 "   -0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   CYS A 325 "    0.072 2.00e-02 2.50e+03
        pdb=" O   CYS A 325 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   SER A 326 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.007 2.00e-02 2.50e+03   2.47e-02 1.22e+01
        pdb=" CG  TYR B 105 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "    0.037 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.032 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2178
        2.80 -     3.33: 8692
        3.33 -     3.85: 14958
        3.85 -     4.38: 17905
        4.38 -     4.90: 30344
  Nonbonded interactions: 74077
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD1 ASN D 304 "
            pdb=" NZ  LYS D 308 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OG  SER H 161 "
            pdb=" O   LYS H 163 "
     model   vdw
     2.360 3.040
  ... (remaining 74072 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.530
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.420
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.173   9024  Z= 0.195
  Angle     :  0.680   9.633  12242  Z= 0.412
  Chirality :  0.045   0.397   1410
  Planarity :  0.007   0.057   1537
  Dihedral  : 12.747  83.080   3172
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.70 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  2.33 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.23), residues: 1127
  helix: -1.09 (0.22), residues: 406
  sheet: -0.18 (0.30), residues: 277
  loop : -1.01 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.053   0.008   ARG A  24 
 TYR   0.037   0.005   TYR B 105 
 PHE   0.022   0.002   PHE D 354 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9022)
  covalent geometry    : angle       0.67968 (12238)
  SS BOND              : bond        0.00401 (    2)
  SS BOND              : angle       1.58853 (    4)
  hydrogen bonds       : bond        0.15273 (  474)
  hydrogen bonds       : angle       6.97626 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 317
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7518 (ttpt)
REVERT: A   33 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6426 (mt-10)
REVERT: A  186 GLU cc_start: 0.6591 (tt0) cc_final: 0.5926 (tt0)
REVERT: A  197 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7524 (mtpp)
REVERT: A  210 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7453 (mmtt)
REVERT: A  243 MET cc_start: 0.7404 (tpp) cc_final: 0.7156 (tpp)
REVERT: A  272 ASP cc_start: 0.7260 (t0) cc_final: 0.6936 (t0)
REVERT: A  330 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6424 (mmtt)
REVERT: B   43 ILE cc_start: 0.8993 (mm) cc_final: 0.8747 (mt)
REVERT: B   83 ASP cc_start: 0.6948 (t0) cc_final: 0.6418 (t0)
REVERT: B  121 CYS cc_start: 0.6087 (t) cc_final: 0.5699 (t)
REVERT: B  188 MET cc_start: 0.7480 (mmm) cc_final: 0.7132 (mmm)
REVERT: B  204 CYS cc_start: 0.7584 (m) cc_final: 0.7309 (m)
REVERT: B  205 ASP cc_start: 0.7097 (p0) cc_final: 0.6852 (p0)
REVERT: B  219 ARG cc_start: 0.6994 (mmt180) cc_final: 0.6775 (mmt-90)
REVERT: B  228 ASP cc_start: 0.5840 (t0) cc_final: 0.5626 (t70)
REVERT: B  232 ILE cc_start: 0.8525 (tt) cc_final: 0.8196 (tt)
REVERT: B  239 ASN cc_start: 0.7401 (m-40) cc_final: 0.7189 (m-40)
REVERT: B  261 LEU cc_start: 0.8006 (mp) cc_final: 0.7803 (mt)
REVERT: B  277 SER cc_start: 0.8371 (t) cc_final: 0.7748 (m)
REVERT: B  312 ASP cc_start: 0.5953 (t0) cc_final: 0.5590 (t70)
REVERT: B  322 ASP cc_start: 0.6255 (t0) cc_final: 0.6038 (t0)
REVERT: B  333 ASP cc_start: 0.6065 (m-30) cc_final: 0.5609 (m-30)
REVERT: D   47 LEU cc_start: 0.7675 (mt) cc_final: 0.7423 (mt)
REVERT: D  178 ILE cc_start: 0.7526 (mt) cc_final: 0.7284 (mt)
REVERT: D  218 PHE cc_start: 0.7195 (t80) cc_final: 0.6946 (t80)
REVERT: D  314 MET cc_start: 0.7046 (tpp) cc_final: 0.6522 (mpp)
REVERT: H   94 TYR cc_start: 0.7747 (m-80) cc_final: 0.7327 (m-80)
REVERT: H  140 MET cc_start: 0.8153 (mmm) cc_final: 0.7888 (mmm)
REVERT: H  173 TYR cc_start: 0.8330 (m-80) cc_final: 0.8067 (m-80)
REVERT: H  178 LEU cc_start: 0.8174 (tp) cc_final: 0.7957 (tt)
REVERT: H  226 VAL cc_start: 0.7971 (t) cc_final: 0.7670 (m)
REVERT: H  243 THR cc_start: 0.8580 (m) cc_final: 0.8336 (p)
  outliers start: 7
  outliers final: 2
  residues processed: 322
  average time/residue: 0.0904
  time to fit residues: 40.0343
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  326 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0670
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.5980
   overall best weight:    1.0120

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** D  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
H 171 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.125328 restraints weight = 12297.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.01
r_work: 0.3474 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9024  Z= 0.166
  Angle     :  0.600   7.363  12242  Z= 0.318
  Chirality :  0.044   0.135   1410
  Planarity :  0.004   0.044   1537
  Dihedral  :  5.531  28.928   1236
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.12 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1127
  helix:  1.00 (0.26), residues: 413
  sheet: -0.23 (0.29), residues: 287
  loop : -0.41 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 137 
 TYR   0.013   0.002   TYR D 370 
 PHE   0.019   0.002   PHE D 218 
 TRP   0.020   0.002   TRP B 339 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9022)
  covalent geometry    : angle       0.59837 (12238)
  SS BOND              : bond        0.00505 (    2)
  SS BOND              : angle       2.39749 (    4)
  hydrogen bonds       : bond        0.03843 (  474)
  hydrogen bonds       : angle       5.12891 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 274
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7558 (mmtt)
REVERT: A   29 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7724 (ttpt)
REVERT: A  186 GLU cc_start: 0.7468 (tt0) cc_final: 0.7216 (tt0)
REVERT: A  197 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7972 (mtmm)
REVERT: A  210 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7289 (mmtt)
REVERT: A  261 ASP cc_start: 0.7926 (t0) cc_final: 0.7708 (t0)
REVERT: A  272 ASP cc_start: 0.7712 (t0) cc_final: 0.7407 (t0)
REVERT: A  330 LYS cc_start: 0.7517 (mmtt) cc_final: 0.6893 (mmtt)
REVERT: B   22 ARG cc_start: 0.7150 (mtt90) cc_final: 0.6900 (mtt90)
REVERT: B   74 SER cc_start: 0.8367 (m) cc_final: 0.8111 (t)
REVERT: B  135 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8115 (m)
REVERT: B  137 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.7720 (mmt180)
REVERT: B  188 MET cc_start: 0.8288 (mmm) cc_final: 0.7867 (mmm)
REVERT: B  205 ASP cc_start: 0.7548 (p0) cc_final: 0.7192 (p0)
REVERT: B  219 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7506 (mmt90)
REVERT: B  230 ASN cc_start: 0.8267 (t0) cc_final: 0.8041 (m-40)
REVERT: B  232 ILE cc_start: 0.8663 (tt) cc_final: 0.8392 (tt)
REVERT: B  261 LEU cc_start: 0.8386 (mp) cc_final: 0.8152 (mp)
REVERT: B  275 SER cc_start: 0.8372 (t) cc_final: 0.8062 (m)
REVERT: B  277 SER cc_start: 0.8560 (t) cc_final: 0.7959 (m)
REVERT: B  312 ASP cc_start: 0.6732 (t0) cc_final: 0.6354 (t70)
REVERT: B  331 SER cc_start: 0.8492 (t) cc_final: 0.8148 (p)
REVERT: B  333 ASP cc_start: 0.7133 (m-30) cc_final: 0.6590 (m-30)
REVERT: D  154 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8071 (p)
REVERT: D  218 PHE cc_start: 0.7681 (t80) cc_final: 0.7230 (t80)
REVERT: H  178 LEU cc_start: 0.8458 (tp) cc_final: 0.8231 (tt)
REVERT: H  243 THR cc_start: 0.8646 (m) cc_final: 0.8294 (p)
  outliers start: 21
  outliers final: 12
  residues processed: 282
  average time/residue: 0.0866
  time to fit residues: 34.0689
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 262
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    0.0980
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 96 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 GLN
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.141668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.124455 restraints weight = 12282.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.02
r_work: 0.3462 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9024  Z= 0.136
  Angle     :  0.554   7.352  12242  Z= 0.292
  Chirality :  0.042   0.132   1410
  Planarity :  0.004   0.048   1537
  Dihedral  :  5.121  27.109   1235
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 14.19 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.25), residues: 1127
  helix:  1.50 (0.26), residues: 406
  sheet: -0.15 (0.29), residues: 294
  loop : -0.16 (0.32), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.020   0.002   TYR D 179 
 PHE   0.017   0.002   PHE D 218 
 TRP   0.016   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9022)
  covalent geometry    : angle       0.55344 (12238)
  SS BOND              : bond        0.00499 (    2)
  SS BOND              : angle       1.90877 (    4)
  hydrogen bonds       : bond        0.03635 (  474)
  hydrogen bonds       : angle       4.82547 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 271
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7483 (tm-30)
REVERT: A   23 LEU cc_start: 0.7536 (mt) cc_final: 0.7253 (mp)
REVERT: A   29 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7310 (ttpt)
REVERT: A   33 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7074 (mt-10)
REVERT: A  186 GLU cc_start: 0.7435 (tt0) cc_final: 0.7055 (tt0)
REVERT: A  197 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8081 (mtpp)
REVERT: A  210 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7365 (mmtt)
REVERT: A  261 ASP cc_start: 0.7828 (t0) cc_final: 0.7617 (t0)
REVERT: A  269 ASN cc_start: 0.8275 (m-40) cc_final: 0.8067 (m-40)
REVERT: A  272 ASP cc_start: 0.7662 (t0) cc_final: 0.7390 (t0)
REVERT: A  330 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7034 (mmtt)
REVERT: B   22 ARG cc_start: 0.7121 (mtt90) cc_final: 0.6881 (mtt90)
REVERT: B   68 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7522 (tpp80)
REVERT: B   74 SER cc_start: 0.8372 (m) cc_final: 0.8139 (t)
REVERT: B  129 ARG cc_start: 0.7148 (mmp80) cc_final: 0.6839 (mmp80)
REVERT: B  135 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8142 (m)
REVERT: B  168 LEU cc_start: 0.7954 (tp) cc_final: 0.7554 (tp)
REVERT: B  188 MET cc_start: 0.8225 (mmm) cc_final: 0.7806 (mmm)
REVERT: B  205 ASP cc_start: 0.7501 (p0) cc_final: 0.7073 (p0)
REVERT: B  219 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7512 (mmt-90)
REVERT: B  239 ASN cc_start: 0.7906 (m-40) cc_final: 0.7570 (m-40)
REVERT: B  258 ASP cc_start: 0.7761 (t70) cc_final: 0.7194 (t0)
REVERT: B  263 THR cc_start: 0.8399 (m) cc_final: 0.8179 (p)
REVERT: B  275 SER cc_start: 0.8338 (t) cc_final: 0.8036 (m)
REVERT: B  277 SER cc_start: 0.8459 (t) cc_final: 0.7849 (m)
REVERT: B  312 ASP cc_start: 0.6799 (t0) cc_final: 0.6458 (t70)
REVERT: B  331 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8133 (p)
REVERT: B  333 ASP cc_start: 0.7080 (m-30) cc_final: 0.6553 (m-30)
REVERT: D   98 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8271 (m-40)
REVERT: D  154 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8144 (p)
REVERT: H   60 TYR cc_start: 0.8216 (m-80) cc_final: 0.7858 (m-80)
REVERT: H   67 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7650 (ttp80)
REVERT: H   93 MET cc_start: 0.7691 (ttm) cc_final: 0.7456 (ttt)
REVERT: H  172 THR cc_start: 0.8623 (m) cc_final: 0.8116 (p)
REVERT: H  243 THR cc_start: 0.8678 (m) cc_final: 0.8309 (p)
  outliers start: 32
  outliers final: 21
  residues processed: 281
  average time/residue: 0.0958
  time to fit residues: 36.7119
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 251
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue   98 ASN
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  174 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 93 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
D  77 ASN
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.123345 restraints weight = 12376.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.05
r_work: 0.3427 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9024  Z= 0.189
  Angle     :  0.582   6.852  12242  Z= 0.303
  Chirality :  0.044   0.138   1410
  Planarity :  0.004   0.047   1537
  Dihedral  :  5.070  26.775   1235
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 15.68 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1127
  helix:  1.58 (0.26), residues: 410
  sheet: -0.31 (0.29), residues: 301
  loop : -0.11 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  32 
 TYR   0.014   0.002   TYR D 179 
 PHE   0.019   0.002   PHE D 198 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 9022)
  covalent geometry    : angle       0.57990 (12238)
  SS BOND              : bond        0.01005 (    2)
  SS BOND              : angle       2.52660 (    4)
  hydrogen bonds       : bond        0.03732 (  474)
  hydrogen bonds       : angle       4.81664 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 275
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7254 (ttpt)
REVERT: A   33 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7168 (mt-10)
REVERT: A  186 GLU cc_start: 0.7470 (tt0) cc_final: 0.7106 (tt0)
REVERT: A  197 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8103 (mtpp)
REVERT: A  210 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7391 (mmtt)
REVERT: A  251 ASP cc_start: 0.7757 (t0) cc_final: 0.7442 (t0)
REVERT: A  261 ASP cc_start: 0.7878 (t0) cc_final: 0.7650 (t0)
REVERT: A  269 ASN cc_start: 0.8283 (m-40) cc_final: 0.8044 (m-40)
REVERT: A  272 ASP cc_start: 0.7632 (t0) cc_final: 0.7328 (t0)
REVERT: A  330 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7078 (mmtt)
REVERT: B   74 SER cc_start: 0.8426 (m) cc_final: 0.8191 (t)
REVERT: B  101 MET cc_start: 0.8491 (ptm) cc_final: 0.8272 (ptp)
REVERT: B  129 ARG cc_start: 0.7231 (mmp80) cc_final: 0.6795 (mmp80)
REVERT: B  135 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8343 (m)
REVERT: B  188 MET cc_start: 0.8277 (mmm) cc_final: 0.7923 (mmm)
REVERT: B  205 ASP cc_start: 0.7492 (p0) cc_final: 0.7050 (p0)
REVERT: B  219 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7554 (mmt-90)
REVERT: B  230 ASN cc_start: 0.8204 (m-40) cc_final: 0.7844 (m110)
REVERT: B  232 ILE cc_start: 0.8678 (tt) cc_final: 0.8463 (tt)
REVERT: B  239 ASN cc_start: 0.7955 (m-40) cc_final: 0.7662 (m-40)
REVERT: B  254 ASP cc_start: 0.7320 (t70) cc_final: 0.6907 (t70)
REVERT: B  258 ASP cc_start: 0.7847 (t70) cc_final: 0.7315 (t0)
REVERT: B  275 SER cc_start: 0.8355 (t) cc_final: 0.8119 (m)
REVERT: B  277 SER cc_start: 0.8407 (t) cc_final: 0.7828 (m)
REVERT: B  298 ASP cc_start: 0.8017 (t70) cc_final: 0.7747 (t70)
REVERT: B  312 ASP cc_start: 0.6968 (t0) cc_final: 0.6647 (t70)
REVERT: B  331 SER cc_start: 0.8331 (t) cc_final: 0.8067 (p)
REVERT: B  333 ASP cc_start: 0.7051 (m-30) cc_final: 0.6630 (m-30)
REVERT: D   98 ASN cc_start: 0.8484 (m110) cc_final: 0.8060 (m-40)
REVERT: D  102 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7791 (t0)
REVERT: D  154 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8188 (p)
REVERT: H   60 TYR cc_start: 0.8243 (m-80) cc_final: 0.7891 (m-80)
REVERT: H   87 ARG cc_start: 0.7433 (ptm160) cc_final: 0.7087 (ptm160)
REVERT: H   93 MET cc_start: 0.7725 (ttm) cc_final: 0.7510 (ttt)
REVERT: H  172 THR cc_start: 0.8580 (m) cc_final: 0.8150 (p)
REVERT: H  178 LEU cc_start: 0.8554 (tp) cc_final: 0.8350 (tt)
REVERT: H  243 THR cc_start: 0.8729 (m) cc_final: 0.8323 (p)
  outliers start: 34
  outliers final: 22
  residues processed: 286
  average time/residue: 0.0974
  time to fit residues: 37.8790
Evaluate side-chains
  297 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 272
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  368 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  174 LEU
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 18 optimal weight:    0.0870
   chunk 19 optimal weight:    0.0970
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   chunk 86 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0970
   chunk 28 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
B 156 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
D 153 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.143377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.126211 restraints weight = 12259.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.04
r_work: 0.3481 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9024  Z= 0.103
  Angle     :  0.530   7.267  12242  Z= 0.276
  Chirality :  0.041   0.156   1410
  Planarity :  0.004   0.046   1537
  Dihedral  :  4.762  25.408   1235
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.27 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1127
  helix:  1.89 (0.26), residues: 410
  sheet: -0.23 (0.29), residues: 299
  loop : -0.09 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  49 
 TYR   0.025   0.001   TYR D 179 
 PHE   0.016   0.001   PHE A 196 
 TRP   0.018   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 9022)
  covalent geometry    : angle       0.52904 (12238)
  SS BOND              : bond        0.00456 (    2)
  SS BOND              : angle       1.35957 (    4)
  hydrogen bonds       : bond        0.03277 (  474)
  hydrogen bonds       : angle       4.73058 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 260
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7245 (ttpt)
REVERT: A   33 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: A   35 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7841 (mtmm)
REVERT: A  186 GLU cc_start: 0.7379 (tt0) cc_final: 0.7048 (tt0)
REVERT: A  197 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8055 (mtpp)
REVERT: A  210 LYS cc_start: 0.7822 (mmmt) cc_final: 0.7442 (mmtt)
REVERT: A  251 ASP cc_start: 0.7739 (t0) cc_final: 0.7430 (t0)
REVERT: A  269 ASN cc_start: 0.8239 (m-40) cc_final: 0.8016 (m-40)
REVERT: A  309 ASP cc_start: 0.7000 (m-30) cc_final: 0.6614 (m-30)
REVERT: A  318 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7093 (mm-30)
REVERT: A  330 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7106 (mmtt)
REVERT: B   22 ARG cc_start: 0.7248 (mtt90) cc_final: 0.7041 (mtt90)
REVERT: B   68 ARG cc_start: 0.7961 (ttt-90) cc_final: 0.7602 (tpp80)
REVERT: B   74 SER cc_start: 0.8427 (m) cc_final: 0.8177 (t)
REVERT: B  127 LYS cc_start: 0.8932 (mttt) cc_final: 0.8685 (mttm)
REVERT: B  129 ARG cc_start: 0.7194 (mmp80) cc_final: 0.6697 (mmp80)
REVERT: B  135 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8201 (m)
REVERT: B  168 LEU cc_start: 0.7946 (tp) cc_final: 0.7492 (tp)
REVERT: B  205 ASP cc_start: 0.7481 (p0) cc_final: 0.7099 (p0)
REVERT: B  219 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7465 (mmt90)
REVERT: B  232 ILE cc_start: 0.8706 (tt) cc_final: 0.8346 (tt)
REVERT: B  239 ASN cc_start: 0.7861 (m-40) cc_final: 0.7410 (m-40)
REVERT: B  258 ASP cc_start: 0.7822 (t70) cc_final: 0.7363 (t0)
REVERT: B  275 SER cc_start: 0.8366 (t) cc_final: 0.8084 (m)
REVERT: B  277 SER cc_start: 0.8219 (t) cc_final: 0.7681 (m)
REVERT: B  298 ASP cc_start: 0.7922 (t70) cc_final: 0.7620 (t70)
REVERT: B  312 ASP cc_start: 0.6756 (t0) cc_final: 0.6436 (t70)
REVERT: B  331 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8187 (p)
REVERT: B  333 ASP cc_start: 0.7042 (m-30) cc_final: 0.6611 (m-30)
REVERT: D   98 ASN cc_start: 0.8525 (m110) cc_final: 0.8297 (m-40)
REVERT: D  154 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8169 (p)
REVERT: G   21 MET cc_start: 0.6432 (tpp) cc_final: 0.6217 (tpp)
REVERT: H   67 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7640 (ttp80)
REVERT: H   93 MET cc_start: 0.7658 (ttm) cc_final: 0.7445 (ttm)
REVERT: H  172 THR cc_start: 0.8493 (m) cc_final: 0.8178 (p)
REVERT: H  178 LEU cc_start: 0.8540 (tp) cc_final: 0.8292 (tt)
REVERT: H  215 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7348 (p)
REVERT: H  243 THR cc_start: 0.8693 (m) cc_final: 0.8236 (p)
  outliers start: 32
  outliers final: 19
  residues processed: 271
  average time/residue: 0.0943
  time to fit residues: 35.2348
Evaluate side-chains
  265 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 242
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 93 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   chunk 107 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
D  77 ASN
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.141629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124663 restraints weight = 12339.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.03
r_work: 0.3464 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9024  Z= 0.126
  Angle     :  0.532   7.320  12242  Z= 0.277
  Chirality :  0.042   0.160   1410
  Planarity :  0.004   0.047   1537
  Dihedral  :  4.665  25.699   1235
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.27 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.26), residues: 1127
  helix:  1.93 (0.26), residues: 419
  sheet: -0.28 (0.29), residues: 293
  loop : -0.10 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.020   0.001   TYR D 179 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9022)
  covalent geometry    : angle       0.53122 (12238)
  SS BOND              : bond        0.00552 (    2)
  SS BOND              : angle       1.78267 (    4)
  hydrogen bonds       : bond        0.03252 (  474)
  hydrogen bonds       : angle       4.66938 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 241
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.7933 (mttt) cc_final: 0.7707 (mmmm)
REVERT: A   29 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7217 (ttpt)
REVERT: A   33 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7141 (mt-10)
REVERT: A   35 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7845 (mtmm)
REVERT: A  186 GLU cc_start: 0.7383 (tt0) cc_final: 0.7013 (tt0)
REVERT: A  197 LYS cc_start: 0.8294 (mtmt) cc_final: 0.8091 (mtpp)
REVERT: A  210 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7620 (mmtt)
REVERT: A  251 ASP cc_start: 0.7741 (t0) cc_final: 0.7434 (t0)
REVERT: A  269 ASN cc_start: 0.8254 (m-40) cc_final: 0.8036 (m-40)
REVERT: A  309 ASP cc_start: 0.6961 (m-30) cc_final: 0.6616 (m-30)
REVERT: A  330 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7129 (mmtt)
REVERT: B   22 ARG cc_start: 0.7270 (mtt90) cc_final: 0.7004 (mtt90)
REVERT: B   74 SER cc_start: 0.8405 (m) cc_final: 0.8175 (t)
REVERT: B  127 LYS cc_start: 0.8969 (mttt) cc_final: 0.8711 (mttm)
REVERT: B  129 ARG cc_start: 0.7207 (mmp80) cc_final: 0.6705 (mmp80)
REVERT: B  135 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8296 (m)
REVERT: B  168 LEU cc_start: 0.7985 (tp) cc_final: 0.7505 (tp)
REVERT: B  188 MET cc_start: 0.8211 (mmm) cc_final: 0.7903 (mmm)
REVERT: B  205 ASP cc_start: 0.7372 (p0) cc_final: 0.7164 (p0)
REVERT: B  232 ILE cc_start: 0.8719 (tt) cc_final: 0.8361 (tt)
REVERT: B  239 ASN cc_start: 0.7768 (m-40) cc_final: 0.7451 (m-40)
REVERT: B  258 ASP cc_start: 0.7716 (t0) cc_final: 0.7246 (t0)
REVERT: B  275 SER cc_start: 0.8377 (t) cc_final: 0.8097 (m)
REVERT: B  277 SER cc_start: 0.8374 (t) cc_final: 0.7828 (m)
REVERT: B  298 ASP cc_start: 0.7924 (t70) cc_final: 0.7567 (t0)
REVERT: B  331 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8091 (p)
REVERT: B  333 ASP cc_start: 0.6996 (m-30) cc_final: 0.6470 (m-30)
REVERT: D   98 ASN cc_start: 0.8503 (m110) cc_final: 0.8245 (m-40)
REVERT: D  102 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7602 (t0)
REVERT: D  154 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8161 (p)
REVERT: H  172 THR cc_start: 0.8511 (m) cc_final: 0.8195 (p)
REVERT: H  178 LEU cc_start: 0.8501 (tp) cc_final: 0.8250 (tt)
REVERT: H  243 THR cc_start: 0.8724 (m) cc_final: 0.8243 (p)
  outliers start: 36
  outliers final: 26
  residues processed: 254
  average time/residue: 0.0927
  time to fit residues: 32.7301
Evaluate side-chains
  262 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  219 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0570
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.127241 restraints weight = 12287.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.06
r_work: 0.3462 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9024  Z= 0.125
  Angle     :  0.544   7.627  12242  Z= 0.280
  Chirality :  0.042   0.175   1410
  Planarity :  0.004   0.048   1537
  Dihedral  :  4.672  26.692   1235
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.17 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.26), residues: 1127
  helix:  1.99 (0.26), residues: 419
  sheet: -0.25 (0.30), residues: 289
  loop : -0.13 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  49 
 TYR   0.018   0.001   TYR D 179 
 PHE   0.023   0.002   PHE H  68 
 TRP   0.016   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9022)
  covalent geometry    : angle       0.54337 (12238)
  SS BOND              : bond        0.00517 (    2)
  SS BOND              : angle       1.71869 (    4)
  hydrogen bonds       : bond        0.03236 (  474)
  hydrogen bonds       : angle       4.73106 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 241
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.7924 (mttt) cc_final: 0.7700 (mmmm)
REVERT: A   29 LYS cc_start: 0.7589 (ttpt) cc_final: 0.7189 (ttpt)
REVERT: A   33 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7155 (mt-10)
REVERT: A   35 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7879 (mtmm)
REVERT: A  186 GLU cc_start: 0.7401 (tt0) cc_final: 0.6972 (tt0)
REVERT: A  210 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7592 (mmtt)
REVERT: A  251 ASP cc_start: 0.7747 (t0) cc_final: 0.7439 (t0)
REVERT: A  269 ASN cc_start: 0.8242 (m-40) cc_final: 0.8040 (m-40)
REVERT: A  309 ASP cc_start: 0.6966 (m-30) cc_final: 0.6693 (m-30)
REVERT: A  318 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7131 (mm-30)
REVERT: A  330 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7223 (mmtt)
REVERT: A  333 GLN cc_start: 0.7954 (tp40) cc_final: 0.7390 (tp-100)
REVERT: B   22 ARG cc_start: 0.7272 (mtt90) cc_final: 0.6990 (mtt90)
REVERT: B   74 SER cc_start: 0.8416 (m) cc_final: 0.8199 (t)
REVERT: B  101 MET cc_start: 0.8316 (ptp) cc_final: 0.8106 (mtm)
REVERT: B  127 LYS cc_start: 0.8959 (mttt) cc_final: 0.8697 (mttm)
REVERT: B  129 ARG cc_start: 0.7236 (mmp80) cc_final: 0.6723 (mmp80)
REVERT: B  135 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8329 (m)
REVERT: B  137 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7648 (mmt180)
REVERT: B  188 MET cc_start: 0.8207 (mmm) cc_final: 0.7751 (mmm)
REVERT: B  239 ASN cc_start: 0.7769 (m-40) cc_final: 0.7325 (m-40)
REVERT: B  256 ARG cc_start: 0.8154 (mpp80) cc_final: 0.7664 (mtm-85)
REVERT: B  258 ASP cc_start: 0.7705 (t0) cc_final: 0.7210 (t0)
REVERT: B  275 SER cc_start: 0.8372 (t) cc_final: 0.8103 (m)
REVERT: B  277 SER cc_start: 0.8348 (t) cc_final: 0.7838 (m)
REVERT: B  298 ASP cc_start: 0.7969 (t70) cc_final: 0.7554 (t0)
REVERT: D   98 ASN cc_start: 0.8493 (m110) cc_final: 0.8200 (m-40)
REVERT: D  102 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7681 (t0)
REVERT: D  121 MET cc_start: 0.7330 (mtm) cc_final: 0.7032 (mtp)
REVERT: D  154 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (p)
REVERT: D  162 ILE cc_start: 0.7664 (mt) cc_final: 0.7347 (tt)
REVERT: H   67 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7616 (ttp80)
REVERT: H  172 THR cc_start: 0.8516 (m) cc_final: 0.8202 (p)
REVERT: H  178 LEU cc_start: 0.8514 (tp) cc_final: 0.8299 (tt)
  outliers start: 32
  outliers final: 23
  residues processed: 251
  average time/residue: 0.0815
  time to fit residues: 29.2812
Evaluate side-chains
  259 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 233
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0670
   chunk 65 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.142303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.125385 restraints weight = 12409.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.04
r_work: 0.3469 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9024  Z= 0.124
  Angle     :  0.565  14.628  12242  Z= 0.287
  Chirality :  0.042   0.191   1410
  Planarity :  0.004   0.048   1537
  Dihedral  :  4.651  28.086   1235
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.92 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.26), residues: 1127
  helix:  2.00 (0.26), residues: 416
  sheet: -0.30 (0.29), residues: 294
  loop : -0.06 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.017   0.001   TYR D 179 
 PHE   0.031   0.002   PHE D 218 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9022)
  covalent geometry    : angle       0.56461 (12238)
  SS BOND              : bond        0.00518 (    2)
  SS BOND              : angle       1.67572 (    4)
  hydrogen bonds       : bond        0.03250 (  474)
  hydrogen bonds       : angle       4.71757 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 235
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7194 (ttpt)
REVERT: A   33 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7192 (mt-10)
REVERT: A   35 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7897 (mtmm)
REVERT: A  197 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8029 (ttmm)
REVERT: A  210 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7491 (mmtt)
REVERT: A  251 ASP cc_start: 0.7713 (t0) cc_final: 0.7444 (t0)
REVERT: A  309 ASP cc_start: 0.6940 (m-30) cc_final: 0.6718 (m-30)
REVERT: A  318 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7126 (mm-30)
REVERT: A  330 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7195 (mmtt)
REVERT: A  333 GLN cc_start: 0.7953 (tp40) cc_final: 0.7367 (tp40)
REVERT: B   22 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6939 (mtt90)
REVERT: B   74 SER cc_start: 0.8418 (m) cc_final: 0.8198 (t)
REVERT: B   87 THR cc_start: 0.8490 (m) cc_final: 0.8235 (m)
REVERT: B  129 ARG cc_start: 0.7226 (mmp80) cc_final: 0.6701 (mmp80)
REVERT: B  135 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8354 (m)
REVERT: B  137 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7723 (mmt180)
REVERT: B  168 LEU cc_start: 0.7744 (tt) cc_final: 0.7502 (tp)
REVERT: B  188 MET cc_start: 0.8064 (mmm) cc_final: 0.7679 (mmm)
REVERT: B  210 LEU cc_start: 0.7959 (tp) cc_final: 0.7758 (tp)
REVERT: B  219 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7304 (mmt90)
REVERT: B  239 ASN cc_start: 0.7701 (m-40) cc_final: 0.7396 (m-40)
REVERT: B  256 ARG cc_start: 0.8130 (mpp80) cc_final: 0.7612 (mtm-85)
REVERT: B  258 ASP cc_start: 0.7701 (t0) cc_final: 0.7160 (t0)
REVERT: B  275 SER cc_start: 0.8379 (t) cc_final: 0.8102 (m)
REVERT: B  277 SER cc_start: 0.8401 (t) cc_final: 0.7921 (m)
REVERT: B  298 ASP cc_start: 0.7979 (t70) cc_final: 0.7531 (t0)
REVERT: D   98 ASN cc_start: 0.8486 (m110) cc_final: 0.8191 (m-40)
REVERT: D  102 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7663 (t0)
REVERT: D  121 MET cc_start: 0.7250 (mtm) cc_final: 0.6960 (mtp)
REVERT: D  154 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8227 (p)
REVERT: D  162 ILE cc_start: 0.7660 (mt) cc_final: 0.7348 (tt)
REVERT: H   59 TYR cc_start: 0.8001 (m-80) cc_final: 0.7728 (m-10)
REVERT: H   67 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7546 (ttp80)
REVERT: H   90 ASP cc_start: 0.7942 (m-30) cc_final: 0.7647 (m-30)
REVERT: H  172 THR cc_start: 0.8504 (m) cc_final: 0.8201 (p)
REVERT: H  178 LEU cc_start: 0.8492 (tp) cc_final: 0.8239 (tt)
REVERT: H  226 VAL cc_start: 0.7922 (t) cc_final: 0.7561 (m)
  outliers start: 29
  outliers final: 23
  residues processed: 246
  average time/residue: 0.0815
  time to fit residues: 28.8834
Evaluate side-chains
  262 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    0.0470
   chunk 36 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0270
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.145622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.128568 restraints weight = 12485.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.09
r_work: 0.3467 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9024  Z= 0.120
  Angle     :  0.551   9.496  12242  Z= 0.282
  Chirality :  0.042   0.184   1410
  Planarity :  0.004   0.048   1537
  Dihedral  :  4.597  29.736   1235
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.23 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.26), residues: 1127
  helix:  2.12 (0.26), residues: 409
  sheet: -0.33 (0.29), residues: 297
  loop : -0.08 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.016   0.001   TYR D 179 
 PHE   0.027   0.001   PHE B 199 
 TRP   0.013   0.002   TRP H 111 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9022)
  covalent geometry    : angle       0.55000 (12238)
  SS BOND              : bond        0.00518 (    2)
  SS BOND              : angle       1.63947 (    4)
  hydrogen bonds       : bond        0.03249 (  474)
  hydrogen bonds       : angle       4.62281 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 241
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7407 (mmtt)
REVERT: A   29 LYS cc_start: 0.7592 (ttpt) cc_final: 0.7207 (ttpt)
REVERT: A   33 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7231 (mt-10)
REVERT: A  197 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8053 (ttmm)
REVERT: A  251 ASP cc_start: 0.7754 (t0) cc_final: 0.7486 (t0)
REVERT: A  309 ASP cc_start: 0.6942 (m-30) cc_final: 0.6726 (m-30)
REVERT: A  318 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7158 (mm-30)
REVERT: A  330 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7329 (mmtt)
REVERT: A  333 GLN cc_start: 0.7956 (tp40) cc_final: 0.7391 (tp40)
REVERT: B   22 ARG cc_start: 0.7298 (mtt90) cc_final: 0.6935 (mtt90)
REVERT: B   74 SER cc_start: 0.8416 (m) cc_final: 0.8180 (t)
REVERT: B   87 THR cc_start: 0.8488 (m) cc_final: 0.8231 (m)
REVERT: B  127 LYS cc_start: 0.8966 (mttt) cc_final: 0.8697 (mttm)
REVERT: B  129 ARG cc_start: 0.7329 (mmp80) cc_final: 0.6810 (mmp80)
REVERT: B  135 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (m)
REVERT: B  150 ARG cc_start: 0.8246 (mmt-90) cc_final: 0.7734 (mmm160)
REVERT: B  188 MET cc_start: 0.8015 (mmm) cc_final: 0.7708 (mmm)
REVERT: B  239 ASN cc_start: 0.7608 (m-40) cc_final: 0.6631 (m-40)
REVERT: B  256 ARG cc_start: 0.8128 (mpp80) cc_final: 0.7192 (mtm-85)
REVERT: B  258 ASP cc_start: 0.7696 (t0) cc_final: 0.6940 (t0)
REVERT: B  275 SER cc_start: 0.8357 (t) cc_final: 0.8120 (m)
REVERT: B  277 SER cc_start: 0.8478 (t) cc_final: 0.7946 (m)
REVERT: B  283 ARG cc_start: 0.8463 (tpt-90) cc_final: 0.8227 (tpt-90)
REVERT: B  298 ASP cc_start: 0.8009 (t70) cc_final: 0.7514 (t70)
REVERT: D   98 ASN cc_start: 0.8538 (m110) cc_final: 0.8253 (m-40)
REVERT: D  102 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7632 (t0)
REVERT: D  121 MET cc_start: 0.7280 (mtm) cc_final: 0.6997 (mtp)
REVERT: D  154 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8235 (p)
REVERT: D  205 MET cc_start: 0.6692 (tpt) cc_final: 0.6172 (tpt)
REVERT: G   50 LEU cc_start: 0.8682 (mt) cc_final: 0.8433 (mp)
REVERT: H   59 TYR cc_start: 0.8006 (m-80) cc_final: 0.7745 (m-10)
REVERT: H  172 THR cc_start: 0.8512 (m) cc_final: 0.8224 (p)
REVERT: H  178 LEU cc_start: 0.8474 (tp) cc_final: 0.8237 (tt)
  outliers start: 28
  outliers final: 22
  residues processed: 252
  average time/residue: 0.0878
  time to fit residues: 31.0369
Evaluate side-chains
  261 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 236
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0980
   chunk 43 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.146121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.129245 restraints weight = 12446.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.08
r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.4200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9024  Z= 0.120
  Angle     :  0.570  11.466  12242  Z= 0.290
  Chirality :  0.043   0.304   1410
  Planarity :  0.004   0.048   1537
  Dihedral  :  4.641  30.710   1235
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.40 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.26), residues: 1127
  helix:  2.17 (0.26), residues: 408
  sheet: -0.38 (0.30), residues: 296
  loop : -0.14 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.026   0.001   TYR B 145 
 PHE   0.025   0.001   PHE D 218 
 TRP   0.014   0.001   TRP H 111 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9022)
  covalent geometry    : angle       0.56925 (12238)
  SS BOND              : bond        0.00494 (    2)
  SS BOND              : angle       1.59571 (    4)
  hydrogen bonds       : bond        0.03207 (  474)
  hydrogen bonds       : angle       4.68804 ( 1317)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 237
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7368 (mmtt)
REVERT: A   29 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7226 (ttpt)
REVERT: A   33 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7176 (mt-10)
REVERT: A  197 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8158 (ttmm)
REVERT: A  251 ASP cc_start: 0.7740 (t0) cc_final: 0.7472 (t0)
REVERT: A  318 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7143 (mm-30)
REVERT: A  330 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7329 (mmtt)
REVERT: A  333 GLN cc_start: 0.7956 (tp40) cc_final: 0.7406 (tp40)
REVERT: B   22 ARG cc_start: 0.7297 (mtt90) cc_final: 0.6924 (mtt90)
REVERT: B   74 SER cc_start: 0.8389 (m) cc_final: 0.8156 (t)
REVERT: B   87 THR cc_start: 0.8489 (m) cc_final: 0.8219 (m)
REVERT: B  127 LYS cc_start: 0.8970 (mttt) cc_final: 0.8699 (mttm)
REVERT: B  129 ARG cc_start: 0.7348 (mmp80) cc_final: 0.6811 (mmp80)
REVERT: B  135 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8369 (m)
REVERT: B  150 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.7759 (mmm160)
REVERT: B  188 MET cc_start: 0.8007 (mmm) cc_final: 0.7726 (mmm)
REVERT: B  219 ARG cc_start: 0.7671 (mmt90) cc_final: 0.7241 (mmt-90)
REVERT: B  239 ASN cc_start: 0.7713 (m-40) cc_final: 0.6474 (m-40)
REVERT: B  256 ARG cc_start: 0.8061 (mpp80) cc_final: 0.7171 (mtm-85)
REVERT: B  258 ASP cc_start: 0.7733 (t0) cc_final: 0.6992 (t0)
REVERT: B  275 SER cc_start: 0.8348 (t) cc_final: 0.8113 (m)
REVERT: B  277 SER cc_start: 0.8468 (t) cc_final: 0.7945 (m)
REVERT: B  283 ARG cc_start: 0.8467 (tpt-90) cc_final: 0.8211 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7997 (t70) cc_final: 0.7445 (t70)
REVERT: D   61 LEU cc_start: 0.7393 (mt) cc_final: 0.7152 (mt)
REVERT: D   98 ASN cc_start: 0.8535 (m110) cc_final: 0.8246 (m-40)
REVERT: D  102 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7659 (t0)
REVERT: D  121 MET cc_start: 0.7306 (mtm) cc_final: 0.7025 (mtp)
REVERT: D  154 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8233 (p)
REVERT: D  162 ILE cc_start: 0.7702 (mt) cc_final: 0.7409 (tt)
REVERT: D  205 MET cc_start: 0.6640 (tpt) cc_final: 0.6133 (tpt)
REVERT: G   50 LEU cc_start: 0.8711 (mt) cc_final: 0.8482 (mp)
REVERT: H   59 TYR cc_start: 0.8015 (m-80) cc_final: 0.7754 (m-10)
REVERT: H   67 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7627 (ttp80)
REVERT: H  172 THR cc_start: 0.8505 (m) cc_final: 0.8232 (p)
REVERT: H  178 LEU cc_start: 0.8481 (tp) cc_final: 0.8247 (tt)
  outliers start: 25
  outliers final: 21
  residues processed: 247
  average time/residue: 0.0887
  time to fit residues: 30.4549
Evaluate side-chains
  255 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 231
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0000
   chunk 7 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 311 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.147720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.130925 restraints weight = 12557.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.08
r_work: 0.3459 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9024  Z= 0.135
  Angle     :  0.578  10.123  12242  Z= 0.295
  Chirality :  0.043   0.256   1410
  Planarity :  0.004   0.049   1537
  Dihedral  :  4.666  31.675   1235
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.29 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1127
  helix:  2.14 (0.26), residues: 408
  sheet: -0.30 (0.30), residues: 287
  loop : -0.32 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  49 
 TYR   0.028   0.001   TYR D 179 
 PHE   0.023   0.002   PHE D 218 
 TRP   0.022   0.002   TRP H 111 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9022)
  covalent geometry    : angle       0.57682 (12238)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       1.80582 (    4)
  hydrogen bonds       : bond        0.03291 (  474)
  hydrogen bonds       : angle       4.68875 ( 1317)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2437.16 seconds
wall clock time: 42 minutes 26.05 seconds (2546.05 seconds total)