Starting phenix.real_space_refine
on Wed Feb  4 07:03:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rkn_24501/02_2026/7rkn_24501.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rkn_24501/02_2026/7rkn_24501.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rkn_24501/02_2026/7rkn_24501.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rkn_24501/02_2026/7rkn_24501.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rkn_24501/02_2026/7rkn_24501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rkn_24501/02_2026/7rkn_24501.map"
  }
  resolution = 3.6
  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=   0.000 sd=   0.004
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      71      5.16       5
     C    5993      2.51       5
     N    1586      2.21       5
     O    1743      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9393
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1736
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2575
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 404
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1761
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "L"
      Number of atoms: 520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 520
          Classifications: {'peptide': 68}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'PCA:plan-2': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 2397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2397
          Classifications: {'peptide': 294}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 283}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.26, per 1000 atoms: 0.24
  Number of scatterers: 9393
  At special positions: 0
  Unit cell: (99.22, 122.18, 128.74, 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      71     16.00
     O    1743      8.00
     N    1586      7.00
     C    5993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L   8 " - pdb=" SG  CYS L  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  12 " - pdb=" SG  CYS L  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  23 " - pdb=" SG  CYS R 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 104 " - pdb=" SG  CYS R 173 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 325.0 milliseconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2262

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      36.4% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.563A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.086A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.512A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
      removed outlier: 3.672A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.776A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.782A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 352
      removed outlier: 4.367A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 4.148A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 4.059A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.633A  pdb=" N   PHE D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 56
      removed outlier: 3.746A  pdb=" N   SER D  55 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY D  56 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 52 through 56'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 4.054A  pdb=" N   THR D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 56 through 68
      removed outlier: 3.661A  pdb=" N   ASP L  60 " --> pdb=" O   GLN L  56 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN L  63 " --> pdb=" O   LYS L  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 25 through 60
      Proline residue:  R  34  - end of helix
      removed outlier: 4.742A  pdb=" N   LEU R  53 " --> pdb=" O   ILE R  49 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 93
      removed outlier: 3.608A  pdb=" N   LEU R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
      Proline residue:  R  87  - end of helix
    Processing helix  chain 'R' and resid 103 through 135
      removed outlier: 3.618A  pdb=" N   ILE R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 164
      Proline residue:  R 161  - end of helix
      removed outlier: 3.639A  pdb=" N   MET R 164 " --> pdb=" O   ILE R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 195
    Processing helix  chain 'R' and resid 197 through 216
    Processing helix  chain 'R' and resid 223 through 240
      removed outlier: 3.797A  pdb=" N   VAL R 227 " --> pdb=" O   LYS R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 257
    Processing helix  chain 'R' and resid 262 through 292
      removed outlier: 3.979A  pdb=" N   CYS R 284 " --> pdb=" O   ALA R 280 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   CYS R 285 " --> pdb=" O   PHE R 281 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU R 286 " --> pdb=" O   CYS R 282 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.795A  pdb=" N   TYR R 291 " --> pdb=" O   ASN R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 306
      removed outlier: 3.802A  pdb=" N   GLU R 301 " --> pdb=" O   LYS R 297 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 4.041A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226
      removed outlier: 6.933A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.698A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.207A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.755A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 6.399A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.717A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.979A  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: 3.841A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 317
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.677A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 23
    Processing sheet with id=AB3, first strand: chain 'D' and resid 143 through 148
    Processing sheet with id=AB4, first strand: chain 'D' and resid 174 through 178
      removed outlier: 6.732A  pdb=" N   TRP D 164 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   TYR D 178 " --> pdb=" O   LEU D 162 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU D 162 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 26 through 29
      removed outlier: 3.951A  pdb=" N   HIS L  26 " --> pdb=" O   GLU L  42 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 167 through 168

    397 hydrogen bonds defined for protein.
    1134 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: 1.40

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2996
        1.34 -     1.46: 2237
        1.46 -     1.58: 4265
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 9596
  Sorted by residual:
  bond pdb=" N   PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.463 -0.118 2.00e-02 2.50e+03 3.49e+01
  bond pdb=" C   ILE R 160 "
       pdb=" N   PRO R 161 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.28e-02 6.10e+03 2.53e+00
  bond pdb=" N   GLU R 308 "
       pdb=" CA  GLU R 308 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.90e-02 2.77e+03 2.10e+00
  bond pdb=" C   ILE R 199 "
       pdb=" N   PRO R 200 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.018 1.30e-02 5.92e+03 2.00e+00
  bond pdb=" CA  THR B  87 "
       pdb=" C   THR B  87 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 1.51e-02 4.39e+03 1.93e+00
  ... (remaining 9591 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12688
        2.75 -     5.49: 271
        5.49 -     8.24: 39
        8.24 -    10.98: 9
       10.98 -    13.73: 2
  Bond angle restraints: 13009
  Sorted by residual:
  angle pdb=" CA  CYS B 121 "
        pdb=" CB  CYS B 121 "
        pdb=" SG  CYS B 121 "
      ideal   model   delta    sigma   weight residual
     114.40  128.13  -13.73 2.30e+00 1.89e-01 3.56e+01
  angle pdb=" C   ARG D 179 "
        pdb=" N   MET D 180 "
        pdb=" CA  MET D 180 "
      ideal   model   delta    sigma   weight residual
     121.54  130.11   -8.57 1.91e+00 2.74e-01 2.01e+01
  angle pdb=" C   ALA R 307 "
        pdb=" N   GLU R 308 "
        pdb=" CA  GLU R 308 "
      ideal   model   delta    sigma   weight residual
     121.70  129.70   -8.00 1.80e+00 3.09e-01 1.98e+01
  angle pdb=" C   GLN L  63 "
        pdb=" N   HIS L  64 "
        pdb=" CA  HIS L  64 "
      ideal   model   delta    sigma   weight residual
     121.58  113.88    7.70 1.95e+00 2.63e-01 1.56e+01
  angle pdb=" CB  MET R 174 "
        pdb=" CG  MET R 174 "
        pdb=" SD  MET R 174 "
      ideal   model   delta    sigma   weight residual
     112.70  123.88  -11.18 3.00e+00 1.11e-01 1.39e+01
  ... (remaining 13004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 5256
       17.61 -    35.22: 353
       35.22 -    52.84: 67
       52.84 -    70.45: 13
       70.45 -    88.06: 7
  Dihedral angle restraints: 5696
    sinusoidal: 2195
      harmonic: 3501
  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
     -86.00 -133.83   47.83     1      1.00e+01 1.00e-02 3.16e+01
  dihedral pdb=" CA  TYR A 296 "
           pdb=" C   TYR A 296 "
           pdb=" N   GLU A 297 "
           pdb=" CA  GLU A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CB  CYS R 104 "
           pdb=" SG  CYS R 104 "
           pdb=" SG  CYS R 173 "
           pdb=" CB  CYS R 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -52.96  -33.04     1      1.00e+01 1.00e-02 1.55e+01
  ... (remaining 5693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1304
       0.086 -    0.171: 164
       0.171 -    0.257: 10
       0.257 -    0.342: 1
       0.342 -    0.428: 1
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CB  ILE A 222 "
            pdb=" CA  ILE A 222 "
            pdb=" CG1 ILE A 222 "
            pdb=" CG2 ILE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.43 2.00e-01 2.50e+01 4.58e+00
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  LYS R  33 "
            pdb=" N   LYS R  33 "
            pdb=" C   LYS R  33 "
            pdb=" CB  LYS R  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 1477 not shown)

  Planarity restraints: 1641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "   -0.038 2.00e-02 2.50e+03   4.38e-02 4.80e+01
        pdb=" CG  TRP B  82 "    0.110 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "   -0.068 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "   -0.017 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R  52 "    0.029 2.00e-02 2.50e+03   5.77e-02 3.33e+01
        pdb=" C   PHE R  52 "   -0.100 2.00e-02 2.50e+03
        pdb=" O   PHE R  52 "    0.037 2.00e-02 2.50e+03
        pdb=" N   LEU R  53 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 320 "    0.018 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   TYR A 320 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   TYR A 320 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR A 321 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1638 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 823
        2.75 -     3.28: 9651
        3.28 -     3.82: 15379
        3.82 -     4.36: 18595
        4.36 -     4.90: 31856
  Nonbonded interactions: 76304
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   LYS A  35 "
            pdb=" OG1 THR A 219 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   GLY D  33 "
            pdb=" OG  SER D  99 "
     model   vdw
     2.283 3.040
  ... (remaining 76299 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.230
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     9.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
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   0.118   9603  Z= 0.217
  Angle     :  0.976  13.731  13023  Z= 0.522
  Chirality :  0.058   0.428   1480
  Planarity :  0.007   0.086   1641
  Dihedral  : 12.675  88.061   3413
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -2.17 (0.24), residues: 1182
  helix: -0.08 (0.26), residues: 377
  sheet: -2.46 (0.31), residues: 249
  loop : -1.85 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 137 
 TYR   0.016   0.002   TYR D 178 
 PHE   0.058   0.003   PHE R  52 
 TRP   0.110   0.003   TRP B  82 
 HIS   0.014   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 9596)
  covalent geometry    : angle       0.97369 (13009)
  SS BOND              : bond        0.00525 (    7)
  SS BOND              : angle       2.23204 (   14)
  hydrogen bonds       : bond        0.15427 (  397)
  hydrogen bonds       : angle       6.94551 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.309 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0948
  time to fit residues: 20.7089
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
A 306 GLN
L  56 GLN
R  51 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.092341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.073644 restraints weight = 23660.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075757 restraints weight = 12055.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.076506 restraints weight = 7873.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.076781 restraints weight = 6522.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.076868 restraints weight = 5861.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9603  Z= 0.185
  Angle     :  0.628  10.939  13023  Z= 0.332
  Chirality :  0.044   0.152   1480
  Planarity :  0.004   0.058   1641
  Dihedral  :  4.861  40.753   1300
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  9.63 %
    Favored  : 88.90 %
  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: -1.90 (0.24), residues: 1182
  helix:  0.36 (0.26), residues: 392
  sheet: -2.28 (0.30), residues: 260
  loop : -1.91 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 190 
 TYR   0.016   0.002   TYR D 178 
 PHE   0.025   0.001   PHE A 334 
 TRP   0.043   0.002   TRP B  82 
 HIS   0.015   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 9596)
  covalent geometry    : angle       0.62622 (13009)
  SS BOND              : bond        0.00466 (    7)
  SS BOND              : angle       1.67372 (   14)
  hydrogen bonds       : bond        0.04175 (  397)
  hydrogen bonds       : angle       5.28333 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.403 
Fit side-chains
REVERT: B  105 TYR cc_start: 0.8907 (t80) cc_final: 0.8616 (t80)
REVERT: B  289 TYR cc_start: 0.8718 (m-80) cc_final: 0.8286 (m-80)
REVERT: D  218 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7650 (ttt)
REVERT: R  302 LEU cc_start: 0.8215 (mm) cc_final: 0.7785 (pp)
  outliers start: 15
  outliers final: 9
  residues processed: 130
  average time/residue: 0.0889
  time to fit residues: 16.7499
Evaluate side-chains
  118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  282 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0170
   chunk 105 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 104 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.5822

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  96 HIS ** 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 = 0.3575 r_free = 0.3575 target = 0.092397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.074217 restraints weight = 24076.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.075815 restraints weight = 13782.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.076626 restraints weight = 9338.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.076644 restraints weight = 7638.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.076791 restraints weight = 7639.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9603  Z= 0.164
  Angle     :  0.592  10.866  13023  Z= 0.312
  Chirality :  0.043   0.153   1480
  Planarity :  0.004   0.043   1641
  Dihedral  :  4.781  43.082   1300
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.49 %
    Favored  : 86.15 %
  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: -1.68 (0.25), residues: 1182
  helix:  0.62 (0.26), residues: 393
  sheet: -2.16 (0.30), residues: 266
  loop : -1.85 (0.28), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 190 
 TYR   0.015   0.001   TYR D 178 
 PHE   0.020   0.001   PHE A 334 
 TRP   0.047   0.002   TRP B  82 
 HIS   0.014   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9596)
  covalent geometry    : angle       0.59048 (13009)
  SS BOND              : bond        0.00507 (    7)
  SS BOND              : angle       1.51304 (   14)
  hydrogen bonds       : bond        0.03751 (  397)
  hydrogen bonds       : angle       4.98312 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  324 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7841 (p)
REVERT: B  289 TYR cc_start: 0.8724 (m-80) cc_final: 0.8312 (m-80)
REVERT: D   76 LYS cc_start: 0.7903 (mttt) cc_final: 0.7536 (tptp)
REVERT: D  218 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7702 (ttt)
  outliers start: 24
  outliers final: 9
  residues processed: 140
  average time/residue: 0.0929
  time to fit residues: 18.5803
Evaluate side-chains
  122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  282 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 112 optimal weight:    9.9990
   chunk 102 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  96 HIS ** 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 = 0.3505 r_free = 0.3505 target = 0.089861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.071249 restraints weight = 24022.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.072758 restraints weight = 13040.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.073612 restraints weight = 8462.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.073817 restraints weight = 7163.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.074059 restraints weight = 6684.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9603  Z= 0.195
  Angle     :  0.608  10.652  13023  Z= 0.320
  Chirality :  0.043   0.155   1480
  Planarity :  0.004   0.047   1641
  Dihedral  :  4.809  41.395   1300
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.95 %
    Favored  : 83.99 %
  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: -1.65 (0.25), residues: 1182
  helix:  0.62 (0.26), residues: 393
  sheet: -2.11 (0.30), residues: 269
  loop : -1.83 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 190 
 TYR   0.015   0.001   TYR D 178 
 PHE   0.016   0.001   PHE A 334 
 TRP   0.021   0.001   TRP R  89 
 HIS   0.015   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 9596)
  covalent geometry    : angle       0.60588 (13009)
  SS BOND              : bond        0.00514 (    7)
  SS BOND              : angle       1.57510 (   14)
  hydrogen bonds       : bond        0.03715 (  397)
  hydrogen bonds       : angle       4.97313 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 TYR cc_start: 0.8476 (m-10) cc_final: 0.8221 (m-80)
REVERT: A  324 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7979 (p)
REVERT: B  130 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8000 (mm-30)
REVERT: B  234 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.9168 (m-80)
REVERT: D  218 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7806 (ttt)
REVERT: R  193 MET cc_start: 0.8399 (ttp) cc_final: 0.8117 (ttm)
  outliers start: 21
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0892
  time to fit residues: 17.3953
Evaluate side-chains
  123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  105 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 115 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0000
   chunk 114 optimal weight:    0.0870
   chunk 89 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.4162

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

Flipped N/Q/H residues before XYZ refinement:
** R  96 HIS ** 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 = 0.3561 r_free = 0.3561 target = 0.093040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.074344 restraints weight = 23868.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.076133 restraints weight = 11924.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.076979 restraints weight = 7769.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.077083 restraints weight = 6898.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.077238 restraints weight = 6420.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9603  Z= 0.108
  Angle     :  0.567   9.639  13023  Z= 0.294
  Chirality :  0.042   0.146   1480
  Planarity :  0.003   0.045   1641
  Dihedral  :  4.564  42.139   1300
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.93 %
    Favored  : 83.10 %
  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: -1.37 (0.25), residues: 1182
  helix:  0.86 (0.26), residues: 393
  sheet: -1.92 (0.31), residues: 263
  loop : -1.71 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 313 
 TYR   0.014   0.001   TYR D 178 
 PHE   0.017   0.001   PHE A 334 
 TRP   0.020   0.001   TRP R  89 
 HIS   0.015   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9596)
  covalent geometry    : angle       0.56598 (13009)
  SS BOND              : bond        0.00462 (    7)
  SS BOND              : angle       1.11084 (   14)
  hydrogen bonds       : bond        0.03442 (  397)
  hydrogen bonds       : angle       4.73509 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 TYR cc_start: 0.8466 (m-10) cc_final: 0.8234 (m-80)
REVERT: B  264 TYR cc_start: 0.9091 (m-80) cc_final: 0.8849 (m-80)
REVERT: D   34 MET cc_start: 0.7618 (mmm) cc_final: 0.7008 (mtm)
REVERT: L   56 GLN cc_start: 0.7922 (mp10) cc_final: 0.7475 (pm20)
REVERT: L   60 ASP cc_start: 0.8494 (t0) cc_final: 0.8291 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0799
  time to fit residues: 16.4980
Evaluate side-chains
  123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain R residue  105 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0770
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    0.2980
   overall best weight:    1.0742

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.090328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.071032 restraints weight = 24726.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.073092 restraints weight = 12750.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.074426 restraints weight = 8332.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.075323 restraints weight = 6321.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.075889 restraints weight = 5267.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9603  Z= 0.131
  Angle     :  0.579   9.880  13023  Z= 0.298
  Chirality :  0.043   0.241   1480
  Planarity :  0.004   0.048   1641
  Dihedral  :  4.510  41.777   1300
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.62 %
    Favored  : 81.93 %
  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: -1.35 (0.25), residues: 1182
  helix:  0.90 (0.26), residues: 393
  sheet: -1.98 (0.30), residues: 291
  loop : -1.61 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 313 
 TYR   0.014   0.001   TYR D 178 
 PHE   0.015   0.001   PHE R 111 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.013   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9596)
  covalent geometry    : angle       0.57732 (13009)
  SS BOND              : bond        0.00442 (    7)
  SS BOND              : angle       1.29280 (   14)
  hydrogen bonds       : bond        0.03437 (  397)
  hydrogen bonds       : angle       4.72721 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  256 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8349 (m110)
REVERT: A  320 TYR cc_start: 0.8490 (m-10) cc_final: 0.8261 (m-80)
REVERT: A  324 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7720 (p)
REVERT: B  130 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8035 (mm-30)
REVERT: D   34 MET cc_start: 0.7706 (mmm) cc_final: 0.7095 (mtm)
REVERT: D  219 GLN cc_start: 0.8103 (pp30) cc_final: 0.7855 (pp30)
REVERT: L   56 GLN cc_start: 0.8105 (mp10) cc_final: 0.7550 (pm20)
REVERT: L   60 ASP cc_start: 0.8632 (t0) cc_final: 0.8377 (t0)
REVERT: R   56 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6285 (t80)
REVERT: R  158 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7356 (tt)
  outliers start: 25
  outliers final: 15
  residues processed: 135
  average time/residue: 0.0864
  time to fit residues: 17.3966
Evaluate side-chains
  129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  158 ILE
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0060
   chunk 116 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0370
   chunk 37 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 85 optimal weight:    7.9990
   overall best weight:    0.4274

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** R  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.093591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075063 restraints weight = 23845.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.077282 restraints weight = 12227.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.077866 restraints weight = 8007.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.077894 restraints weight = 6582.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.078602 restraints weight = 6290.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9603  Z= 0.108
  Angle     :  0.568   9.401  13023  Z= 0.292
  Chirality :  0.042   0.203   1480
  Planarity :  0.003   0.047   1641
  Dihedral  :  4.423  41.906   1300
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.52 %
    Favored  : 81.34 %
  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: -1.19 (0.25), residues: 1182
  helix:  1.05 (0.26), residues: 393
  sheet: -1.88 (0.30), residues: 285
  loop : -1.56 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  44 
 TYR   0.013   0.001   TYR D 178 
 PHE   0.018   0.001   PHE R 111 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.014   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9596)
  covalent geometry    : angle       0.56745 (13009)
  SS BOND              : bond        0.00445 (    7)
  SS BOND              : angle       1.08443 (   14)
  hydrogen bonds       : bond        0.03320 (  397)
  hydrogen bonds       : angle       4.64106 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8339 (m110)
REVERT: A  324 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7615 (p)
REVERT: B   51 LEU cc_start: 0.3615 (OUTLIER) cc_final: 0.3322 (tt)
REVERT: L   56 GLN cc_start: 0.7917 (mp10) cc_final: 0.7518 (pm20)
REVERT: R   56 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6291 (t80)
REVERT: R  158 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7355 (tt)
  outliers start: 32
  outliers final: 21
  residues processed: 143
  average time/residue: 0.0856
  time to fit residues: 18.2963
Evaluate side-chains
  136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   64 HIS
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  158 ILE
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 103 optimal weight:   30.0000
   chunk 96 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** R  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.093115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.074754 restraints weight = 23805.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.076881 restraints weight = 12074.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.077402 restraints weight = 7993.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.077466 restraints weight = 6740.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.078097 restraints weight = 6400.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9603  Z= 0.120
  Angle     :  0.576   9.695  13023  Z= 0.297
  Chirality :  0.042   0.186   1480
  Planarity :  0.004   0.046   1641
  Dihedral  :  4.355  41.999   1300
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.91 %
    Favored  : 80.94 %
  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: -1.14 (0.25), residues: 1182
  helix:  1.11 (0.26), residues: 391
  sheet: -1.78 (0.30), residues: 285
  loop : -1.58 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  44 
 TYR   0.015   0.001   TYR D 178 
 PHE   0.016   0.001   PHE R 111 
 TRP   0.031   0.001   TRP B  82 
 HIS   0.013   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9596)
  covalent geometry    : angle       0.57091 (13009)
  SS BOND              : bond        0.00508 (    7)
  SS BOND              : angle       2.37798 (   14)
  hydrogen bonds       : bond        0.03323 (  397)
  hydrogen bonds       : angle       4.63957 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8104 (tt)
REVERT: A  256 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8404 (m110)
REVERT: A  324 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7639 (p)
REVERT: D   76 LYS cc_start: 0.7749 (pttt) cc_final: 0.7144 (tptp)
REVERT: L   56 GLN cc_start: 0.7954 (mp10) cc_final: 0.7532 (pm20)
REVERT: L   60 ASP cc_start: 0.8267 (t0) cc_final: 0.7987 (t0)
REVERT: R   56 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6243 (t80)
REVERT: R  168 LYS cc_start: 0.7504 (tptp) cc_final: 0.6580 (tptt)
  outliers start: 32
  outliers final: 23
  residues processed: 140
  average time/residue: 0.0829
  time to fit residues: 17.5451
Evaluate side-chains
  139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   64 HIS
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
A 256 ASN
** R  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.090845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.072340 restraints weight = 23955.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.074681 restraints weight = 12119.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.075202 restraints weight = 7842.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.075508 restraints weight = 6533.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075554 restraints weight = 6312.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9603  Z= 0.175
  Angle     :  0.622  10.234  13023  Z= 0.322
  Chirality :  0.044   0.241   1480
  Planarity :  0.004   0.049   1641
  Dihedral  :  4.582  42.440   1300
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.70 %
    Favored  : 80.55 %
  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: -1.25 (0.25), residues: 1182
  helix:  0.98 (0.26), residues: 389
  sheet: -1.77 (0.30), residues: 289
  loop : -1.63 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.015   0.001   TYR D 178 
 PHE   0.013   0.001   PHE R 111 
 TRP   0.023   0.002   TRP R  89 
 HIS   0.013   0.001   HIS L  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 9596)
  covalent geometry    : angle       0.61812 (13009)
  SS BOND              : bond        0.00467 (    7)
  SS BOND              : angle       2.13413 (   14)
  hydrogen bonds       : bond        0.03492 (  397)
  hydrogen bonds       : angle       4.75020 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8176 (tt)
REVERT: A  324 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7862 (p)
REVERT: D   76 LYS cc_start: 0.7599 (pttt) cc_final: 0.7245 (tptp)
REVERT: D  219 GLN cc_start: 0.8126 (pp30) cc_final: 0.7778 (pp30)
REVERT: L   56 GLN cc_start: 0.8038 (mp10) cc_final: 0.7695 (pm20)
REVERT: L   60 ASP cc_start: 0.8322 (t0) cc_final: 0.7788 (t0)
REVERT: R   56 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6304 (t80)
  outliers start: 28
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0871
  time to fit residues: 17.1850
Evaluate side-chains
  132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  300 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** R  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 300 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.090715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.072071 restraints weight = 23980.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.074315 restraints weight = 12229.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.074649 restraints weight = 8006.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.074753 restraints weight = 6832.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.075367 restraints weight = 6589.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9603  Z= 0.180
  Angle     :  0.630  10.269  13023  Z= 0.328
  Chirality :  0.044   0.221   1480
  Planarity :  0.004   0.049   1641
  Dihedral  :  4.614  42.404   1300
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.99 %
    Favored  : 80.65 %
  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: -1.30 (0.25), residues: 1182
  helix:  0.89 (0.26), residues: 389
  sheet: -1.79 (0.30), residues: 289
  loop : -1.63 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 313 
 TYR   0.015   0.001   TYR D 178 
 PHE   0.013   0.001   PHE R 111 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9596)
  covalent geometry    : angle       0.62721 (13009)
  SS BOND              : bond        0.00501 (    7)
  SS BOND              : angle       2.04235 (   14)
  hydrogen bonds       : bond        0.03654 (  397)
  hydrogen bonds       : angle       4.77668 ( 1134)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8156 (tt)
REVERT: A  324 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7882 (p)
REVERT: D   76 LYS cc_start: 0.7602 (pttt) cc_final: 0.7225 (tptp)
REVERT: D  219 GLN cc_start: 0.8121 (pp30) cc_final: 0.7787 (pp30)
REVERT: L   56 GLN cc_start: 0.8075 (mp10) cc_final: 0.7734 (pm20)
REVERT: R   56 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6278 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 127
  average time/residue: 0.0835
  time to fit residues: 15.8194
Evaluate side-chains
  127 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 85 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0870
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.9562

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

Flipped N/Q/H residues before XYZ refinement:
** R  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 300 GLN ** 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 = 0.3544 r_free = 0.3544 target = 0.091984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.073442 restraints weight = 23817.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.075777 restraints weight = 12162.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076213 restraints weight = 7873.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.076280 restraints weight = 6625.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.076906 restraints weight = 6343.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9603  Z= 0.132
  Angle     :  0.604   9.687  13023  Z= 0.312
  Chirality :  0.043   0.191   1480
  Planarity :  0.004   0.047   1641
  Dihedral  :  4.537  41.611   1300
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.09 %
    Favored  : 80.55 %
  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: -1.21 (0.25), residues: 1182
  helix:  0.98 (0.26), residues: 387
  sheet: -1.70 (0.30), residues: 289
  loop : -1.62 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 313 
 TYR   0.014   0.001   TYR D 178 
 PHE   0.015   0.001   PHE R 111 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9596)
  covalent geometry    : angle       0.60052 (13009)
  SS BOND              : bond        0.00537 (    7)
  SS BOND              : angle       2.01150 (   14)
  hydrogen bonds       : bond        0.03575 (  397)
  hydrogen bonds       : angle       4.75373 ( 1134)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1677.90 seconds
wall clock time: 29 minutes 56.64 seconds (1796.64 seconds total)