Starting phenix.real_space_refine
on Fri Aug 22 19:19:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6gdg_4390/08_2025/6gdg_4390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6gdg_4390/08_2025/6gdg_4390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6gdg_4390/08_2025/6gdg_4390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6gdg_4390/08_2025/6gdg_4390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6gdg_4390/08_2025/6gdg_4390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6gdg_4390/08_2025/6gdg_4390.cif"
  }
  resolution = 4.11
  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=   0.001 sd=   0.012
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      49      5.16       5
     C    4611      2.51       5
     N    1246      2.21       5
     O    1317      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7223
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1913
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 9, 'TRANS': 254}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 161
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 98
    Chain: "B"
      Number of atoms: 2377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2377
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 206
          Unresolved non-hydrogen angles: 252
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 5, 'ARG:plan': 14, 'GLU:plan': 7, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 157
    Chain: "C"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 262
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 41}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "D"
      Number of atoms: 1721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1721
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 155
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 98
    Chain: "E"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 928
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'NEC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.01, per 1000 atoms: 0.28
  Number of scatterers: 7223
  At special positions: 0
  Unit cell: (92.02, 125.19, 78.11, 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      49     16.00
     O    1317      8.00
     N    1246      7.00
     C    4611      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " 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: 0.65
  Conformation dependent library (CDL) restraints added in 443.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1874

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      42.8% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 34
      removed outlier: 3.853A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 59
      removed outlier: 3.510A  pdb=" N   PHE A  44 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 69
      removed outlier: 3.791A  pdb=" N   ILE A  66 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLY A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 108
      removed outlier: 3.612A  pdb=" N   ILE A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 117 through 137
    Processing helix  chain 'A' and resid 167 through 172
      removed outlier: 3.635A  pdb=" N   VAL A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
    Processing helix  chain 'A' and resid 180 through 186
    Processing helix  chain 'A' and resid 186 through 209
      removed outlier: 3.673A  pdb=" N   LYS A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 259
      removed outlier: 3.782A  pdb=" N   PHE A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      Proline residue:  A 248  - end of helix
    Processing helix  chain 'A' and resid 266 through 288
      removed outlier: 3.858A  pdb=" N   ASN A 280 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   SER A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A 282 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 292 through 299
      removed outlier: 3.719A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 12 through 24
      removed outlier: 3.865A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
    Processing helix  chain 'D' and resid 13 through 40
      removed outlier: 3.803A  pdb=" N   LYS D  17 " --> pdb=" O   ARG D  13 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS D  25 " --> pdb=" O   GLU D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 57
      removed outlier: 4.071A  pdb=" N   ILE D  56 " --> pdb=" O   GLY D  52 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL D  57 " --> pdb=" O   LYS D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 52 through 57'
    Processing helix  chain 'D' and resid 234 through 238
    Processing helix  chain 'D' and resid 252 through 269
      removed outlier: 3.813A  pdb=" N   GLN D 257 " --> pdb=" O   TYR D 253 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLU D 258 " --> pdb=" O   ASN D 254 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 283 through 294
      removed outlier: 3.520A  pdb=" N   LYS D 290 " --> pdb=" O   LEU D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 302
      removed outlier: 4.118A  pdb=" N   TYR D 301 " --> pdb=" O   LYS D 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 308
      removed outlier: 3.529A  pdb=" N   ALA D 306 " --> pdb=" O   PRO D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 341
      removed outlier: 3.546A  pdb=" N   ILE D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE D 335 " --> pdb=" O   ILE D 331 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE D 338 " --> pdb=" O   GLU D 334 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 381
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.581A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.616A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.657A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.920A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.649A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 4.021A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.066A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 233 through 234
      removed outlier: 3.706A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.657A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 44
      removed outlier: 6.719A  pdb=" N   HIS D  41 " --> pdb=" O   HIS D 220 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   PHE D 222 " --> pdb=" O   HIS D  41 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU D  43 " --> pdb=" O   PHE D 222 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE D 212 " --> pdb=" O   PHE D 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 243 through 244
    Processing sheet with id=AB1, first strand: chain 'D' and resid 247 through 249
    Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.626A  pdb=" N   SER E  71 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.549A  pdb=" N   THR E 122 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1083 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: 1.18

  Time building geometry restraints manager: 0.88 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: 2335
        1.34 -     1.46: 906
        1.46 -     1.58: 4070
        1.58 -     1.70: 0
        1.70 -     1.81: 65
  Bond restraints: 7376
  Sorted by residual:
  bond pdb=" C4  NEC A 400 "
       pdb=" C5  NEC A 400 "
    ideal  model  delta    sigma   weight residual
    1.385  1.474 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C5  NEC A 400 "
       pdb=" C6  NEC A 400 "
    ideal  model  delta    sigma   weight residual
    1.407  1.488 -0.081 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" CA  VAL A 188 "
       pdb=" CB  VAL A 188 "
    ideal  model  delta    sigma   weight residual
    1.539  1.560 -0.021 5.40e-03 3.43e+04 1.47e+01
  bond pdb=" C8  NEC A 400 "
       pdb=" N7  NEC A 400 "
    ideal  model  delta    sigma   weight residual
    1.302  1.359 -0.057 2.00e-02 2.50e+03 8.12e+00
  bond pdb=" CA  ILE A  64 "
       pdb=" CB  ILE A  64 "
    ideal  model  delta    sigma   weight residual
    1.540  1.571 -0.031 1.25e-02 6.40e+03 6.01e+00
  ... (remaining 7371 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 9227
        1.97 -     3.94: 807
        3.94 -     5.92: 41
        5.92 -     7.89: 4
        7.89 -     9.86: 3
  Bond angle restraints: 10082
  Sorted by residual:
  angle pdb=" N   ASP D 229 "
        pdb=" CA  ASP D 229 "
        pdb=" C   ASP D 229 "
      ideal   model   delta    sigma   weight residual
     112.38  118.19   -5.81 1.22e+00 6.72e-01 2.26e+01
  angle pdb=" CA  VAL A 188 "
        pdb=" C   VAL A 188 "
        pdb=" N   PRO A 189 "
      ideal   model   delta    sigma   weight residual
     120.83  118.29    2.54 6.10e-01 2.69e+00 1.73e+01
  angle pdb=" N   SER B 161 "
        pdb=" CA  SER B 161 "
        pdb=" C   SER B 161 "
      ideal   model   delta    sigma   weight residual
     108.38  113.47   -5.09 1.35e+00 5.49e-01 1.42e+01
  angle pdb=" C   PHE D 302 "
        pdb=" N   PRO D 303 "
        pdb=" CA  PRO D 303 "
      ideal   model   delta    sigma   weight residual
     119.47  123.82   -4.35 1.16e+00 7.43e-01 1.40e+01
  angle pdb=" N   THR E 104 "
        pdb=" CA  THR E 104 "
        pdb=" C   THR E 104 "
      ideal   model   delta    sigma   weight residual
     108.38  113.31   -4.93 1.35e+00 5.49e-01 1.34e+01
  ... (remaining 10077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 3959
       16.99 -    33.99: 266
       33.99 -    50.98: 66
       50.98 -    67.97: 12
       67.97 -    84.96: 4
  Dihedral angle restraints: 4307
    sinusoidal: 1411
      harmonic: 2896
  Sorted by residual:
  dihedral pdb=" CB  CYS A  74 "
           pdb=" SG  CYS A  74 "
           pdb=" SG  CYS A 146 "
           pdb=" CB  CYS A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.96  -84.96     1      1.00e+01 1.00e-02 8.76e+01
  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 -163.29   77.29     1      1.00e+01 1.00e-02 7.49e+01
  dihedral pdb=" CA  THR B 159 "
           pdb=" C   THR B 159 "
           pdb=" N   SER B 160 "
           pdb=" CA  SER B 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.75   18.25     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 4304 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 703
       0.044 -    0.087: 338
       0.087 -    0.131: 105
       0.131 -    0.174: 37
       0.174 -    0.218: 15
  Chirality restraints: 1198
  Sorted by residual:
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  TRP D 234 "
            pdb=" N   TRP D 234 "
            pdb=" C   TRP D 234 "
            pdb=" CB  TRP D 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1195 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 188 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.25e+00
        pdb=" N   PRO A 189 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 284 "   -0.033 5.00e-02 4.00e+02   5.04e-02 4.07e+00
        pdb=" N   PRO A 285 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 138 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO A 139 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 139 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 139 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 2865
        2.94 -     3.43: 7370
        3.43 -     3.92: 11934
        3.92 -     4.41: 13287
        4.41 -     4.90: 22747
  Nonbonded interactions: 58203
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.449 3.040
  nonbonded pdb=" OG1 THR E 104 "
            pdb=" OD1 ASP E 106 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" OH  TYR E  32 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" O   TYR B 145 "
            pdb=" N   GLY B 162 "
     model   vdw
     2.509 3.120
  nonbonded pdb=" O   GLN D 380 "
            pdb=" OE1 GLU D 382 "
     model   vdw
     2.537 3.040
  ... (remaining 58198 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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.860
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
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      :  0.008   0.089   7381  Z= 0.546
  Angle     :  1.102   9.859  10092  Z= 0.739
  Chirality :  0.061   0.218   1198
  Planarity :  0.004   0.052   1283
  Dihedral  : 13.001  79.978   2418
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 0.72
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.89 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  6.80 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.21), residues: 981
  helix: -1.30 (0.21), residues: 357
  sheet: -2.83 (0.35), residues: 135
  loop : -2.46 (0.23), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 291 
 TYR   0.009   0.001   TYR B 124 
 PHE   0.014   0.002   PHE D 208 
 TRP   0.017   0.001   TRP D 234 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 ( 7376)
  covalent geometry    : angle       1.10276 (10082)
  SS BOND              : bond        0.00417 (    5)
  SS BOND              : angle       0.42834 (   10)
  hydrogen bonds       : bond        0.25478 (  378)
  hydrogen bonds       : angle       9.54611 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 306
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 VAL cc_start: 0.8227 (t) cc_final: 0.7849 (p)
REVERT: A   34 ASN cc_start: 0.7194 (t0) cc_final: 0.6900 (t0)
REVERT: A   38 GLN cc_start: 0.8132 (pt0) cc_final: 0.7557 (pt0)
REVERT: A   82 CYS cc_start: 0.8532 (m) cc_final: 0.8010 (t)
REVERT: A  129 TRP cc_start: 0.6886 (m100) cc_final: 0.6671 (m-10)
REVERT: A  135 ILE cc_start: 0.8309 (mt) cc_final: 0.8091 (tt)
REVERT: A  145 ASN cc_start: 0.7660 (t0) cc_final: 0.6839 (p0)
REVERT: A  193 MET cc_start: 0.7549 (mtp) cc_final: 0.7347 (mtm)
REVERT: A  199 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7934 (ttp-110)
REVERT: A  290 TYR cc_start: 0.8656 (t80) cc_final: 0.8406 (t80)
REVERT: B  111 TYR cc_start: 0.8582 (m-80) cc_final: 0.8201 (m-80)
REVERT: B  125 ASN cc_start: 0.7963 (t0) cc_final: 0.7606 (p0)
REVERT: B  187 VAL cc_start: 0.8688 (t) cc_final: 0.8405 (t)
REVERT: B  218 CYS cc_start: 0.8586 (t) cc_final: 0.8335 (t)
REVERT: B  290 ASP cc_start: 0.7257 (m-30) cc_final: 0.7033 (m-30)
REVERT: B  325 MET cc_start: 0.8631 (ttm) cc_final: 0.8105 (tpt)
REVERT: C   21 MET cc_start: 0.6129 (ttm) cc_final: 0.5835 (mmm)
REVERT: D   17 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8709 (tppt)
REVERT: D  252 ASP cc_start: 0.8738 (m-30) cc_final: 0.8306 (t0)
REVERT: D  268 ASN cc_start: 0.9355 (m-40) cc_final: 0.9154 (m-40)
REVERT: D  270 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8146 (ttt90)
REVERT: D  272 LEU cc_start: 0.9230 (mt) cc_final: 0.9007 (mp)
REVERT: D  334 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: D  346 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8735 (mtp85)
REVERT: D  361 ASN cc_start: 0.8566 (m-40) cc_final: 0.8265 (m110)
REVERT: D  383 LEU cc_start: 0.7660 (tp) cc_final: 0.7437 (mt)
REVERT: E   20 LEU cc_start: 0.7879 (mt) cc_final: 0.7590 (mt)
REVERT: E   60 TYR cc_start: 0.9074 (m-80) cc_final: 0.8525 (m-80)
REVERT: E   68 PHE cc_start: 0.8183 (m-10) cc_final: 0.6736 (m-10)
REVERT: E   69 THR cc_start: 0.8530 (m) cc_final: 0.8164 (p)
REVERT: E   72 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7621 (ttm110)
REVERT: E   74 ASN cc_start: 0.6871 (m-40) cc_final: 0.6050 (t0)
REVERT: E   80 TYR cc_start: 0.7377 (m-80) cc_final: 0.6911 (m-80)
  outliers start: 14
  outliers final: 4
  residues processed: 315
  average time/residue: 0.0910
  time to fit residues: 37.7748
Evaluate side-chains
  189 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 185
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A  38 GLN
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  19 GLN
D 257 GLN
D 347 HIS
E  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.121915 restraints weight = 14746.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.124207 restraints weight = 9319.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.125880 restraints weight = 6631.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126863 restraints weight = 5177.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127869 restraints weight = 4373.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
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      :  0.003   0.046   7381  Z= 0.149
  Angle     :  0.627   9.643  10092  Z= 0.336
  Chirality :  0.044   0.156   1198
  Planarity :  0.005   0.066   1283
  Dihedral  :  5.462  34.032   1084
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.55 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.25), residues: 981
  helix:  0.64 (0.25), residues: 371
  sheet: -2.10 (0.32), residues: 195
  loop : -1.73 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 228 
 TYR   0.029   0.002   TYR B  59 
 PHE   0.013   0.002   PHE D 330 
 TRP   0.018   0.002   TRP B 339 
 HIS   0.017   0.002   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7376)
  covalent geometry    : angle       0.62474 (10082)
  SS BOND              : bond        0.00680 (    5)
  SS BOND              : angle       1.61860 (   10)
  hydrogen bonds       : bond        0.04885 (  378)
  hydrogen bonds       : angle       5.88041 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7775 (t0) cc_final: 0.7071 (p0)
REVERT: A  182 PHE cc_start: 0.8412 (t80) cc_final: 0.7966 (t80)
REVERT: B  166 CYS cc_start: 0.7901 (m) cc_final: 0.7620 (m)
REVERT: B  188 MET cc_start: 0.7736 (mmm) cc_final: 0.6864 (mmm)
REVERT: B  230 ASN cc_start: 0.7817 (m-40) cc_final: 0.7523 (m110)
REVERT: C   36 ASP cc_start: 0.7362 (t0) cc_final: 0.7134 (t70)
REVERT: D   17 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8516 (tppt)
REVERT: D  233 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8056 (mmmt)
REVERT: D  239 ASN cc_start: 0.8391 (p0) cc_final: 0.7888 (p0)
REVERT: D  274 THR cc_start: 0.8168 (p) cc_final: 0.7830 (p)
REVERT: D  298 ILE cc_start: 0.7905 (mp) cc_final: 0.7668 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0740
  time to fit residues: 23.5048
Evaluate side-chains
  154 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 34 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 94 optimal weight:    8.9990
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
B 156 GLN
E  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.133716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118570 restraints weight = 14611.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120427 restraints weight = 9846.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121847 restraints weight = 7357.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122516 restraints weight = 5957.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.123340 restraints weight = 5211.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7381  Z= 0.180
  Angle     :  0.634  11.506  10092  Z= 0.335
  Chirality :  0.044   0.158   1198
  Planarity :  0.005   0.061   1283
  Dihedral  :  5.176  35.422   1084
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.25), residues: 981
  helix:  1.16 (0.26), residues: 366
  sheet: -1.83 (0.32), residues: 203
  loop : -1.37 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 228 
 TYR   0.026   0.002   TYR B  59 
 PHE   0.021   0.002   PHE A 257 
 TRP   0.022   0.002   TRP B 332 
 HIS   0.007   0.002   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 7376)
  covalent geometry    : angle       0.62640 (10082)
  SS BOND              : bond        0.00629 (    5)
  SS BOND              : angle       3.18235 (   10)
  hydrogen bonds       : bond        0.04460 (  378)
  hydrogen bonds       : angle       5.54170 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7775 (t0) cc_final: 0.7038 (p0)
REVERT: A  182 PHE cc_start: 0.8449 (t80) cc_final: 0.8148 (t80)
REVERT: A  237 ILE cc_start: 0.7839 (tt) cc_final: 0.7505 (tp)
REVERT: A  276 LEU cc_start: 0.9362 (tp) cc_final: 0.8811 (tp)
REVERT: B  166 CYS cc_start: 0.7926 (m) cc_final: 0.7658 (m)
REVERT: B  188 MET cc_start: 0.7765 (mmm) cc_final: 0.7258 (mmm)
REVERT: B  230 ASN cc_start: 0.7688 (m-40) cc_final: 0.7438 (m110)
REVERT: C   36 ASP cc_start: 0.7122 (t0) cc_final: 0.6919 (t70)
REVERT: D   17 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8487 (tppt)
REVERT: D  222 PHE cc_start: 0.5850 (t80) cc_final: 0.4375 (t80)
REVERT: D  233 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8440 (mmtt)
REVERT: D  239 ASN cc_start: 0.8461 (p0) cc_final: 0.8065 (p0)
REVERT: D  369 CYS cc_start: 0.8217 (m) cc_final: 0.7867 (m)
REVERT: E   79 LEU cc_start: 0.8534 (tp) cc_final: 0.8265 (tp)
REVERT: E  125 THR cc_start: 0.7595 (p) cc_final: 0.7368 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0784
  time to fit residues: 20.8325
Evaluate side-chains
  152 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0870
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.134689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.118648 restraints weight = 15001.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.120745 restraints weight = 9606.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.122365 restraints weight = 6964.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.123425 restraints weight = 5488.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.124253 restraints weight = 4635.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7381  Z= 0.143
  Angle     :  0.577   6.356  10092  Z= 0.310
  Chirality :  0.043   0.213   1198
  Planarity :  0.004   0.053   1283
  Dihedral  :  4.956  27.215   1084
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.26), residues: 981
  helix:  1.45 (0.27), residues: 367
  sheet: -1.60 (0.32), residues: 214
  loop : -1.09 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 137 
 TYR   0.022   0.001   TYR B  59 
 PHE   0.031   0.002   PHE B 292 
 TRP   0.034   0.002   TRP B 339 
 HIS   0.004   0.001   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7376)
  covalent geometry    : angle       0.57632 (10082)
  SS BOND              : bond        0.00155 (    5)
  SS BOND              : angle       1.16792 (   10)
  hydrogen bonds       : bond        0.04015 (  378)
  hydrogen bonds       : angle       5.26744 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7734 (t0) cc_final: 0.6933 (p0)
REVERT: A  182 PHE cc_start: 0.8556 (t80) cc_final: 0.8312 (t80)
REVERT: A  237 ILE cc_start: 0.7752 (tt) cc_final: 0.7540 (tp)
REVERT: A  276 LEU cc_start: 0.9316 (tp) cc_final: 0.8764 (tp)
REVERT: B  188 MET cc_start: 0.7719 (mmm) cc_final: 0.6495 (mmm)
REVERT: B  296 VAL cc_start: 0.9009 (t) cc_final: 0.8768 (t)
REVERT: C   36 ASP cc_start: 0.7315 (t0) cc_final: 0.7108 (t70)
REVERT: D   17 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8513 (tppt)
REVERT: D  222 PHE cc_start: 0.5743 (t80) cc_final: 0.4222 (t80)
REVERT: D  233 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8273 (mmmt)
REVERT: E  125 THR cc_start: 0.7778 (p) cc_final: 0.7497 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0775
  time to fit residues: 20.6575
Evaluate side-chains
  145 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0000
   chunk 79 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0000
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:    0.3948

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 253 ASN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.138298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.122850 restraints weight = 14507.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.124775 restraints weight = 9631.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.126262 restraints weight = 7137.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.127067 restraints weight = 5700.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.127950 restraints weight = 4927.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.4488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7381  Z= 0.118
  Angle     :  0.568   5.910  10092  Z= 0.300
  Chirality :  0.043   0.182   1198
  Planarity :  0.004   0.053   1283
  Dihedral  :  4.762  31.023   1084
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.11 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.27), residues: 981
  helix:  1.61 (0.27), residues: 369
  sheet: -1.41 (0.33), residues: 210
  loop : -0.88 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 137 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.032   0.002   PHE E  68 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7376)
  covalent geometry    : angle       0.56364 (10082)
  SS BOND              : bond        0.00452 (    5)
  SS BOND              : angle       2.24653 (   10)
  hydrogen bonds       : bond        0.03723 (  378)
  hydrogen bonds       : angle       5.09111 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7774 (t0) cc_final: 0.6988 (p0)
REVERT: A  182 PHE cc_start: 0.8582 (t80) cc_final: 0.8362 (t80)
REVERT: A  237 ILE cc_start: 0.7721 (tt) cc_final: 0.7422 (tp)
REVERT: A  245 CYS cc_start: 0.8166 (m) cc_final: 0.7964 (m)
REVERT: A  276 LEU cc_start: 0.9285 (tp) cc_final: 0.8829 (tp)
REVERT: B  188 MET cc_start: 0.7783 (mmm) cc_final: 0.7249 (mmm)
REVERT: B  230 ASN cc_start: 0.7790 (m-40) cc_final: 0.7183 (m110)
REVERT: B  308 LEU cc_start: 0.8303 (mt) cc_final: 0.7524 (mt)
REVERT: D   17 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8498 (tppt)
REVERT: D  222 PHE cc_start: 0.5542 (t80) cc_final: 0.4210 (t80)
REVERT: D  233 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8389 (mmtt)
REVERT: E  125 THR cc_start: 0.7687 (p) cc_final: 0.7471 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0822
  time to fit residues: 21.0860
Evaluate side-chains
  140 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 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 = 0.3778 r_free = 0.3778 target = 0.137906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.122211 restraints weight = 14626.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.124064 restraints weight = 9879.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.125458 restraints weight = 7431.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.126567 restraints weight = 6043.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.127110 restraints weight = 5146.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7381  Z= 0.126
  Angle     :  0.575   7.204  10092  Z= 0.303
  Chirality :  0.043   0.188   1198
  Planarity :  0.004   0.052   1283
  Dihedral  :  4.683  33.296   1084
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.27), residues: 981
  helix:  1.68 (0.27), residues: 368
  sheet: -1.21 (0.33), residues: 211
  loop : -0.85 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  72 
 TYR   0.020   0.001   TYR B  59 
 PHE   0.037   0.002   PHE E  68 
 TRP   0.011   0.001   TRP D 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7376)
  covalent geometry    : angle       0.57209 (10082)
  SS BOND              : bond        0.00289 (    5)
  SS BOND              : angle       1.81872 (   10)
  hydrogen bonds       : bond        0.03688 (  378)
  hydrogen bonds       : angle       4.93962 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7768 (t0) cc_final: 0.7019 (p0)
REVERT: A  237 ILE cc_start: 0.7619 (tt) cc_final: 0.7391 (tp)
REVERT: A  276 LEU cc_start: 0.9280 (tp) cc_final: 0.8831 (tp)
REVERT: B   51 LEU cc_start: 0.7085 (mp) cc_final: 0.6603 (mp)
REVERT: B  188 MET cc_start: 0.7845 (mmm) cc_final: 0.6880 (mmm)
REVERT: B  230 ASN cc_start: 0.7829 (m-40) cc_final: 0.7395 (m110)
REVERT: D   17 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8481 (tppt)
REVERT: D  222 PHE cc_start: 0.5505 (t80) cc_final: 0.4124 (t80)
REVERT: D  233 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8181 (mmmt)
REVERT: E  125 THR cc_start: 0.7783 (p) cc_final: 0.7526 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0827
  time to fit residues: 21.3134
Evaluate side-chains
  144 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 63 optimal weight:    9.9990
   chunk 22 optimal weight:    0.2980
   chunk 34 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    4.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
A 253 ASN
B  54 HIS
** D  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.126877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111931 restraints weight = 15235.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113615 restraints weight = 10332.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.114841 restraints weight = 7807.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.115865 restraints weight = 6367.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116300 restraints weight = 5500.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.5173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.090   7381  Z= 0.308
  Angle     :  0.782  12.732  10092  Z= 0.411
  Chirality :  0.049   0.286   1198
  Planarity :  0.005   0.053   1283
  Dihedral  :  5.484  39.302   1084
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.27), residues: 981
  helix:  1.30 (0.28), residues: 361
  sheet: -1.46 (0.33), residues: 216
  loop : -1.06 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 199 
 TYR   0.034   0.003   TYR B  59 
 PHE   0.032   0.003   PHE A 257 
 TRP   0.018   0.003   TRP D 271 
 HIS   0.007   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 ( 7376)
  covalent geometry    : angle       0.77864 (10082)
  SS BOND              : bond        0.00354 (    5)
  SS BOND              : angle       2.32203 (   10)
  hydrogen bonds       : bond        0.04729 (  378)
  hydrogen bonds       : angle       5.52366 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7583 (t0) cc_final: 0.7226 (t0)
REVERT: A  145 ASN cc_start: 0.7770 (t0) cc_final: 0.6975 (p0)
REVERT: A  237 ILE cc_start: 0.7726 (tt) cc_final: 0.7480 (tp)
REVERT: A  274 ILE cc_start: 0.8052 (mt) cc_final: 0.7716 (pt)
REVERT: A  276 LEU cc_start: 0.9411 (tp) cc_final: 0.8999 (tp)
REVERT: B  188 MET cc_start: 0.7701 (mmm) cc_final: 0.6716 (mmm)
REVERT: B  230 ASN cc_start: 0.7944 (m-40) cc_final: 0.7655 (m110)
REVERT: B  308 LEU cc_start: 0.8487 (mt) cc_final: 0.8239 (mt)
REVERT: D   17 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8585 (tppt)
REVERT: D  222 PHE cc_start: 0.5826 (t80) cc_final: 0.4379 (t80)
REVERT: D  224 VAL cc_start: 0.8899 (m) cc_final: 0.8620 (t)
REVERT: D  233 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8216 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0774
  time to fit residues: 18.8088
Evaluate side-chains
  132 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 27 optimal weight:   30.0000
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 253 ASN
D  19 GLN
E   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.116191 restraints weight = 15061.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.117989 restraints weight = 10063.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.119523 restraints weight = 7525.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120462 restraints weight = 6057.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.121222 restraints weight = 5206.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7381  Z= 0.155
  Angle     :  0.620   6.306  10092  Z= 0.332
  Chirality :  0.045   0.234   1198
  Planarity :  0.004   0.051   1283
  Dihedral  :  5.118  35.869   1084
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.27), residues: 981
  helix:  1.54 (0.28), residues: 365
  sheet: -1.24 (0.34), residues: 215
  loop : -0.90 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 199 
 TYR   0.021   0.002   TYR B  59 
 PHE   0.021   0.002   PHE D 330 
 TRP   0.025   0.002   TRP B  82 
 HIS   0.007   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7376)
  covalent geometry    : angle       0.61755 (10082)
  SS BOND              : bond        0.00383 (    5)
  SS BOND              : angle       1.93626 (   10)
  hydrogen bonds       : bond        0.04134 (  378)
  hydrogen bonds       : angle       5.23109 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7542 (t0) cc_final: 0.7233 (t0)
REVERT: A  145 ASN cc_start: 0.7842 (t0) cc_final: 0.6968 (p0)
REVERT: A  193 MET cc_start: 0.7483 (mtp) cc_final: 0.7233 (mtm)
REVERT: A  241 LEU cc_start: 0.8176 (mp) cc_final: 0.7640 (mp)
REVERT: A  274 ILE cc_start: 0.7980 (mt) cc_final: 0.7599 (pt)
REVERT: B  188 MET cc_start: 0.7732 (mmm) cc_final: 0.7094 (mmm)
REVERT: B  230 ASN cc_start: 0.7806 (m-40) cc_final: 0.7591 (m110)
REVERT: D   17 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8511 (tppt)
REVERT: D  222 PHE cc_start: 0.5653 (t80) cc_final: 0.4346 (t80)
REVERT: D  233 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8341 (mmtt)
REVERT: E  125 THR cc_start: 0.8339 (m) cc_final: 0.8053 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0773
  time to fit residues: 19.1733
Evaluate side-chains
  139 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0370
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.8066

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

Flipped N/Q/H residues before XYZ refinement:
A 253 ASN
B 311 HIS
D 220 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.129981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115394 restraints weight = 14877.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.116948 restraints weight = 10190.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.118321 restraints weight = 7784.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.119325 restraints weight = 6332.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.119595 restraints weight = 5420.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.5469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7381  Z= 0.207
  Angle     :  0.659   9.437  10092  Z= 0.350
  Chirality :  0.045   0.234   1198
  Planarity :  0.005   0.051   1283
  Dihedral  :  5.242  36.878   1084
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.27), residues: 981
  helix:  1.56 (0.28), residues: 364
  sheet: -1.22 (0.35), residues: 217
  loop : -0.94 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 199 
 TYR   0.022   0.002   TYR B  59 
 PHE   0.016   0.002   PHE E 103 
 TRP   0.013   0.002   TRP A 246 
 HIS   0.005   0.002   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 7376)
  covalent geometry    : angle       0.65648 (10082)
  SS BOND              : bond        0.00271 (    5)
  SS BOND              : angle       2.00253 (   10)
  hydrogen bonds       : bond        0.04203 (  378)
  hydrogen bonds       : angle       5.26551 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7611 (t0) cc_final: 0.7310 (t0)
REVERT: A   86 VAL cc_start: 0.7802 (t) cc_final: 0.7527 (p)
REVERT: A  145 ASN cc_start: 0.7887 (t0) cc_final: 0.7044 (p0)
REVERT: A  193 MET cc_start: 0.7497 (mtp) cc_final: 0.7277 (mtm)
REVERT: A  241 LEU cc_start: 0.8091 (mp) cc_final: 0.7495 (mp)
REVERT: A  245 CYS cc_start: 0.8136 (m) cc_final: 0.7805 (m)
REVERT: A  274 ILE cc_start: 0.8028 (mt) cc_final: 0.7671 (pt)
REVERT: B   51 LEU cc_start: 0.7290 (mp) cc_final: 0.7065 (mp)
REVERT: B  188 MET cc_start: 0.7609 (mmm) cc_final: 0.7310 (mmm)
REVERT: B  230 ASN cc_start: 0.7883 (m-40) cc_final: 0.7544 (m110)
REVERT: B  293 ASN cc_start: 0.7999 (m-40) cc_final: 0.7104 (p0)
REVERT: B  296 VAL cc_start: 0.8901 (t) cc_final: 0.8672 (t)
REVERT: D   17 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8498 (tppt)
REVERT: D  222 PHE cc_start: 0.5612 (t80) cc_final: 0.4337 (t80)
REVERT: D  233 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8521 (mmtt)
REVERT: E  125 THR cc_start: 0.8234 (m) cc_final: 0.7654 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0768
  time to fit residues: 17.6193
Evaluate side-chains
  132 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:   30.0000
   chunk 30 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 253 ASN
E  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.133445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.118697 restraints weight = 14709.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.120547 restraints weight = 9919.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.121951 restraints weight = 7398.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.122806 restraints weight = 5966.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.123321 restraints weight = 5148.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7381  Z= 0.151
  Angle     :  0.617   8.811  10092  Z= 0.325
  Chirality :  0.044   0.221   1198
  Planarity :  0.004   0.050   1283
  Dihedral  :  5.149  44.942   1084
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.27), residues: 981
  helix:  1.65 (0.27), residues: 365
  sheet: -1.08 (0.36), residues: 206
  loop : -0.95 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 199 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.023   0.002   PHE D 330 
 TRP   0.019   0.002   TRP B 339 
 HIS   0.005   0.001   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7376)
  covalent geometry    : angle       0.61472 (10082)
  SS BOND              : bond        0.00327 (    5)
  SS BOND              : angle       1.87696 (   10)
  hydrogen bonds       : bond        0.03912 (  378)
  hydrogen bonds       : angle       5.10890 ( 1083)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7481 (t0) cc_final: 0.7262 (t0)
REVERT: A  145 ASN cc_start: 0.7853 (t0) cc_final: 0.7029 (p0)
REVERT: A  193 MET cc_start: 0.7406 (mtp) cc_final: 0.7129 (mtm)
REVERT: A  241 LEU cc_start: 0.8122 (mp) cc_final: 0.7527 (mp)
REVERT: A  245 CYS cc_start: 0.8166 (m) cc_final: 0.7835 (m)
REVERT: B  234 PHE cc_start: 0.8828 (m-80) cc_final: 0.8404 (m-80)
REVERT: B  293 ASN cc_start: 0.7985 (m-40) cc_final: 0.7044 (p0)
REVERT: B  323 ASP cc_start: 0.7568 (p0) cc_final: 0.7335 (p0)
REVERT: D   17 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8475 (tppt)
REVERT: D   27 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: E  125 THR cc_start: 0.7998 (m) cc_final: 0.7605 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0691
  time to fit residues: 16.2134
Evaluate side-chains
  130 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 60 optimal weight:    0.5980
   chunk 27 optimal weight:   30.0000
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0770
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 253 ASN
B 230 ASN
** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 374 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.135607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.121051 restraints weight = 14736.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122897 restraints weight = 9855.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.124340 restraints weight = 7328.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125141 restraints weight = 5889.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125483 restraints weight = 5091.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7381  Z= 0.127
  Angle     :  0.593   7.917  10092  Z= 0.313
  Chirality :  0.043   0.215   1198
  Planarity :  0.004   0.050   1283
  Dihedral  :  4.869  42.333   1084
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.27), residues: 981
  helix:  1.69 (0.27), residues: 368
  sheet: -0.97 (0.35), residues: 210
  loop : -0.85 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  42 
 TYR   0.008   0.001   TYR E  95 
 PHE   0.017   0.002   PHE E 103 
 TRP   0.012   0.002   TRP B 339 
 HIS   0.007   0.001   HIS D 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7376)
  covalent geometry    : angle       0.59141 (10082)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       1.68394 (   10)
  hydrogen bonds       : bond        0.03756 (  378)
  hydrogen bonds       : angle       5.00989 ( 1083)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1268.84 seconds
wall clock time: 22 minutes 38.37 seconds (1358.37 seconds total)