Starting phenix.real_space_refine
on Sat Apr  4 23:54:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p89_71369/04_2026/9p89_71369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p89_71369/04_2026/9p89_71369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p89_71369/04_2026/9p89_71369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p89_71369/04_2026/9p89_71369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p89_71369/04_2026/9p89_71369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p89_71369/04_2026/9p89_71369.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      23      5.16       5
     C    3834      2.51       5
     N    1144      2.21       5
     O    1127      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6131
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2040
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 238}
          Link IDs: {'PTRANS': 8, 'TRANS': 340}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 877
          Unresolved non-hydrogen angles: 1107
          Unresolved non-hydrogen dihedrals: 715
          Unresolved non-hydrogen chiralities: 69
          Planarities with less than four sites: {'ASP:plan': 23, 'GLU:plan': 29, 'ARG:plan': 21, 'ASN:plan1': 10, 'GLN:plan1': 14, 'PHE:plan': 4, 'TYR:plan': 12, 'HIS:plan': 3, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 517
    Chain: "B"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2235
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 114}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 335
          Unresolved non-hydrogen angles: 426
          Unresolved non-hydrogen dihedrals: 246
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 25, 'GLN:plan1': 8, 'ARG:plan': 9, 'ASN:plan1': 6, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 210
    Chain: "G"
      Number of atoms: 334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 334
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "L"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 35
          Classifications: {'peptide': 5}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 1455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 1455
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 236}
          Link IDs: {'PTRANS': 9, 'TRANS': 275}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 885
          Unresolved non-hydrogen angles: 1160
          Unresolved non-hydrogen dihedrals: 743
          Unresolved non-hydrogen chiralities: 106
          Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 12, 'TYR:plan': 16, 'PHE:plan': 18, 'ARG:plan': 15, 'GLN:plan1': 6, 'HIS:plan': 9, 'GLU:plan': 4, 'TRP:plan': 4}
          Unresolved non-hydrogen planarities: 473
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.61, per 1000 atoms: 0.26
  Number of scatterers: 6131
  At special positions: 0
  Unit cell: (71.4, 96.6, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P       3     15.00
     O    1127      8.00
     N    1144      7.00
     C    3834      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " 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: 0.72
  Conformation dependent library (CDL) restraints added in 370.8 milliseconds
  

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      50.5% 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 11 through 38
      removed outlier: 4.194A  pdb=" N   ARG A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 68 through 97
      removed outlier: 4.316A  pdb=" N   LYS A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LEU A  78 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 116
      removed outlier: 3.660A  pdb=" N   LYS A 107 " --> pdb=" O   TYR A 103 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 138
    Processing helix  chain 'A' and resid 138 through 147
      removed outlier: 3.580A  pdb=" N   GLN A 142 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 163
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 246 through 261
    Processing helix  chain 'A' and resid 262 through 265
    Processing helix  chain 'A' and resid 275 through 286
      removed outlier: 4.065A  pdb=" N   TYR A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 291
      removed outlier: 3.728A  pdb=" N   ASP A 290 " --> pdb=" O   HIS A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 333 through 354
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 25
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 59 through 90
    Processing helix  chain 'R' and resid 98 through 127
      removed outlier: 3.918A  pdb=" N   MET R 120 " --> pdb=" O   LEU R 116 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 137 through 172
      removed outlier: 3.748A  pdb=" N   ARG R 142 " --> pdb=" O   ASP R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 207
      Proline residue:  R 202  - end of helix
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 269
    Processing helix  chain 'R' and resid 294 through 329
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 3.705A  pdb=" N   SER R 356 " --> pdb=" O   LEU R 352 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   THR R 358 " --> pdb=" O   TYR R 354 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
      removed outlier: 4.520A  pdb=" N   VAL R 367 " --> pdb=" O   LEU R 363 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   SER R 368 " --> pdb=" O   TYR R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 375
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.054A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU A  43 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 270 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.054A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU A  43 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 270 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL A 269 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   HIS A 327 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU A 271 " --> pdb=" O   HIS A 327 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47
      removed outlier: 4.191A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47
      removed outlier: 4.191A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.872A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.872A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.602A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153
      removed outlier: 7.121A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.524A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.788A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.540A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 210 through 211

    468 hydrogen bonds defined for protein.
    1362 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: 1.04

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1657
        1.33 -     1.45: 1044
        1.45 -     1.57: 3480
        1.57 -     1.69: 5
        1.69 -     1.81: 31
  Bond restraints: 6217
  Sorted by residual:
  bond pdb=" C   ALA A 342 "
       pdb=" O   ALA A 342 "
    ideal  model  delta    sigma   weight residual
    1.237  1.281 -0.045 1.17e-02 7.31e+03 1.46e+01
  bond pdb=" N   ILE A 337 "
       pdb=" CA  ILE A 337 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.87e+00
  bond pdb=" N   VAL A 344 "
       pdb=" CA  VAL A 344 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.48e+00
  bond pdb=" N   ASP A 321 "
       pdb=" CA  ASP A 321 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.17e-02 7.31e+03 8.36e+00
  bond pdb=" N   VAL A 314 "
       pdb=" CA  VAL A 314 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.34e+00
  ... (remaining 6212 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 8440
        2.52 -     5.05: 122
        5.05 -     7.57: 14
        7.57 -    10.09: 10
       10.09 -    12.62: 4
  Bond angle restraints: 8590
  Sorted by residual:
  angle pdb=" PA  GTP A 401 "
        pdb=" O3A GTP A 401 "
        pdb=" PB  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  133.12  -12.62 3.00e+00 1.11e-01 1.77e+01
  angle pdb=" N   ILE R 128 "
        pdb=" CA  ILE R 128 "
        pdb=" C   ILE R 128 "
      ideal   model   delta    sigma   weight residual
     112.96  109.06    3.90 1.00e+00 1.00e+00 1.52e+01
  angle pdb=" C1' GTP A 401 "
        pdb=" C2' GTP A 401 "
        pdb=" C3' GTP A 401 "
      ideal   model   delta    sigma   weight residual
     111.00  100.05   10.95 3.00e+00 1.11e-01 1.33e+01
  angle pdb=" PB  GTP A 401 "
        pdb=" O3B GTP A 401 "
        pdb=" PG  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  131.02  -10.52 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" CA  LEU G  19 "
        pdb=" CB  LEU G  19 "
        pdb=" CG  LEU G  19 "
      ideal   model   delta    sigma   weight residual
     116.30  128.05  -11.75 3.50e+00 8.16e-02 1.13e+01
  ... (remaining 8585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.10: 3546
       35.10 -    70.19: 47
       70.19 -   105.29: 3
      105.29 -   140.39: 3
      140.39 -   175.48: 1
  Dihedral angle restraints: 3600
    sinusoidal: 608
      harmonic: 2992
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.51   68.51     1      1.00e+01 1.00e-02 6.08e+01
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88   89.61 -175.48     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -34.45  139.04     1      2.00e+01 2.50e-03 4.21e+01
  ... (remaining 3597 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 771
       0.046 -    0.092: 236
       0.092 -    0.137: 60
       0.137 -    0.183: 16
       0.183 -    0.229: 4
  Chirality restraints: 1087
  Sorted by residual:
  chirality pdb=" C3' GTP A 401 "
            pdb=" C2' GTP A 401 "
            pdb=" C4' GTP A 401 "
            pdb=" O3' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.70    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ILE A 323 "
            pdb=" N   ILE A 323 "
            pdb=" C   ILE A 323 "
            pdb=" CB  ILE A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  LEU A 316 "
            pdb=" N   LEU A 316 "
            pdb=" C   LEU A 316 "
            pdb=" CB  LEU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.94e-01
  ... (remaining 1084 not shown)

  Planarity restraints: 1152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG L   9 "    0.061 5.00e-02 4.00e+02   9.19e-02 1.35e+01
        pdb=" N   PRO L  10 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO L  10 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO L  10 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 338 "    0.317 9.50e-02 1.11e+02   1.42e-01 1.24e+01
        pdb=" NE  ARG A 338 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 338 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 338 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 338 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 106 "    0.057 5.00e-02 4.00e+02   8.60e-02 1.18e+01
        pdb=" N   PRO B 107 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "    0.047 5.00e-02 4.00e+02
  ... (remaining 1149 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1232
        2.77 -     3.30: 6167
        3.30 -     3.84: 10194
        3.84 -     4.37: 10036
        4.37 -     4.90: 18016
  Nonbonded interactions: 45645
  Sorted by model distance:
  nonbonded pdb=" N   GLN A 303 "
            pdb=" OE1 GLN A 303 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   THR B  47 "
            pdb=" OG1 THR B  47 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" N   LEU A 239 "
            pdb=" O   GLU A 245 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OG  SER B 279 "
            pdb=" O   LEU B 284 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" O   CYS B 149 "
            pdb=" NH1 ARG B 150 "
     model   vdw
     2.377 3.120
  ... (remaining 45640 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:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.150
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6218  Z= 0.315
  Angle     :  0.837  12.616   8592  Z= 0.494
  Chirality :  0.049   0.229   1087
  Planarity :  0.007   0.142   1152
  Dihedral  : 14.730 175.485   1639
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 30.69 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.27), residues: 1010
  helix:  2.66 (0.22), residues: 509
  sheet: -1.72 (0.38), residues: 157
  loop : -1.29 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 256 
 TYR   0.010   0.001   TYR B 264 
 PHE   0.026   0.002   PHE B 199 
 TRP   0.017   0.002   TRP B 297 
 HIS   0.007   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 6217)
  covalent geometry    : angle       0.83617 ( 8590)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       2.92047 (    2)
  hydrogen bonds       : bond        0.13969 (  450)
  hydrogen bonds       : angle       5.57843 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0646
  time to fit residues: 8.1123
Evaluate side-chains
  79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:   40.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.149293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.116348 restraints weight = 15352.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.117376 restraints weight = 13512.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.118812 restraints weight = 9757.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.119040 restraints weight = 8361.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.119659 restraints weight = 7887.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6218  Z= 0.141
  Angle     :  0.568   7.643   8592  Z= 0.292
  Chirality :  0.041   0.171   1087
  Planarity :  0.005   0.067   1152
  Dihedral  :  9.939 161.020   1067
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 26.35 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.27), residues: 1010
  helix:  2.78 (0.22), residues: 519
  sheet: -1.55 (0.38), residues: 165
  loop : -1.30 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 256 
 TYR   0.010   0.001   TYR A 325 
 PHE   0.037   0.002   PHE A 264 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.012   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6217)
  covalent geometry    : angle       0.56728 ( 8590)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       1.80219 (    2)
  hydrogen bonds       : bond        0.03699 (  450)
  hydrogen bonds       : angle       4.36754 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7883 (p0) cc_final: 0.7682 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0613
  time to fit residues: 7.8033
Evaluate side-chains
  84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  169 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 72 optimal weight:   50.0000
   chunk 88 optimal weight:   40.0000
   chunk 82 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0050
   chunk 13 optimal weight:    0.9980
   chunk 92 optimal weight:   40.0000
   chunk 96 optimal weight:    7.9990
   overall best weight:    0.7794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.150908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.125666 restraints weight = 15037.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.126326 restraints weight = 14406.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.126703 restraints weight = 13797.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.127779 restraints weight = 8580.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.128496 restraints weight = 7254.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6218  Z= 0.105
  Angle     :  0.511   7.304   8592  Z= 0.259
  Chirality :  0.040   0.161   1087
  Planarity :  0.004   0.059   1152
  Dihedral  :  9.340 157.343   1067
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 25.63 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.28), residues: 1010
  helix:  3.13 (0.22), residues: 513
  sheet: -1.30 (0.40), residues: 160
  loop : -1.19 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 256 
 TYR   0.009   0.001   TYR A 235 
 PHE   0.011   0.001   PHE A 272 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.008   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 6217)
  covalent geometry    : angle       0.51082 ( 8590)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       1.09054 (    2)
  hydrogen bonds       : bond        0.03066 (  450)
  hydrogen bonds       : angle       3.92814 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7921 (p0) cc_final: 0.7703 (p0)
REVERT: B  289 TYR cc_start: 0.6423 (m-10) cc_final: 0.6029 (m-10)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0667
  time to fit residues: 8.4874
Evaluate side-chains
  84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 75 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0970
   chunk 61 optimal weight:    0.2980
   chunk 19 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.150880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.125979 restraints weight = 15114.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.124886 restraints weight = 14853.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.125652 restraints weight = 14570.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.126543 restraints weight = 9516.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.128281 restraints weight = 7922.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6218  Z= 0.096
  Angle     :  0.505   7.993   8592  Z= 0.255
  Chirality :  0.040   0.153   1087
  Planarity :  0.004   0.054   1152
  Dihedral  :  9.147 158.214   1067
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 28.88 %
    Favored  : 66.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.28), residues: 1010
  helix:  3.29 (0.22), residues: 513
  sheet: -1.26 (0.40), residues: 161
  loop : -1.15 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 256 
 TYR   0.008   0.001   TYR B 289 
 PHE   0.018   0.001   PHE A 194 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 6217)
  covalent geometry    : angle       0.50513 ( 8590)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.72707 (    2)
  hydrogen bonds       : bond        0.02888 (  450)
  hydrogen bonds       : angle       3.72074 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7794 (p0) cc_final: 0.7536 (p0)
REVERT: B  126 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5817 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0670
  time to fit residues: 7.9474
Evaluate side-chains
  84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:   50.0000
   chunk 32 optimal weight:    0.0970
   chunk 35 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   overall best weight:    2.6184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.144001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.108936 restraints weight = 15452.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.111126 restraints weight = 10951.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.112717 restraints weight = 8675.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.113862 restraints weight = 7402.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.114409 restraints weight = 6630.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6218  Z= 0.201
  Angle     :  0.604   8.371   8592  Z= 0.315
  Chirality :  0.042   0.173   1087
  Planarity :  0.004   0.056   1152
  Dihedral  :  9.453 163.052   1067
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  9.75 %
    Allowed  : 23.10 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.28), residues: 1010
  helix:  2.94 (0.23), residues: 519
  sheet: -1.26 (0.40), residues: 165
  loop : -1.31 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 256 
 TYR   0.015   0.001   TYR B 145 
 PHE   0.023   0.002   PHE A 272 
 TRP   0.020   0.002   TRP B 297 
 HIS   0.010   0.002   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6217)
  covalent geometry    : angle       0.60383 ( 8590)
  SS BOND              : bond        0.00247 (    1)
  SS BOND              : angle       0.88745 (    2)
  hydrogen bonds       : bond        0.03750 (  450)
  hydrogen bonds       : angle       4.08621 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.8079 (p0) cc_final: 0.7861 (p0)
REVERT: B  126 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5889 (tt)
  outliers start: 27
  outliers final: 16
  residues processed: 94
  average time/residue: 0.0631
  time to fit residues: 8.4095
Evaluate side-chains
  89 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 85 optimal weight:   20.0000
   chunk 92 optimal weight:    0.0170
   chunk 97 optimal weight:   40.0000
   chunk 51 optimal weight:   10.0000
   chunk 3 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0040
   chunk 10 optimal weight:   40.0000
   chunk 73 optimal weight:   60.0000
   overall best weight:    0.8232

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.146559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.123295 restraints weight = 15339.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.123225 restraints weight = 17112.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.124880 restraints weight = 14608.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.125342 restraints weight = 9384.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.126443 restraints weight = 8346.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6218  Z= 0.103
  Angle     :  0.532   8.069   8592  Z= 0.269
  Chirality :  0.040   0.152   1087
  Planarity :  0.004   0.052   1152
  Dihedral  :  9.272 167.604   1067
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 26.35 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.28), residues: 1010
  helix:  3.26 (0.22), residues: 514
  sheet: -1.11 (0.40), residues: 164
  loop : -1.18 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 306 
 TYR   0.008   0.001   TYR B 264 
 PHE   0.017   0.002   PHE B 292 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6217)
  covalent geometry    : angle       0.53164 ( 8590)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.42481 (    2)
  hydrogen bonds       : bond        0.03039 (  450)
  hydrogen bonds       : angle       3.70421 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ARG cc_start: 0.7972 (ttt-90) cc_final: 0.7671 (ttt-90)
REVERT: A  313 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6253 (t80)
REVERT: B   76 ASP cc_start: 0.7812 (p0) cc_final: 0.7559 (p0)
REVERT: B   93 ILE cc_start: 0.7858 (mm) cc_final: 0.7596 (mt)
REVERT: B  126 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5848 (tt)
  outliers start: 17
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0638
  time to fit residues: 8.0474
Evaluate side-chains
  86 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:   30.0000
   chunk 32 optimal weight:    0.2980
   chunk 57 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   overall best weight:    3.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B 142 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 = 0.4121 r_free = 0.4121 target = 0.139770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.115326 restraints weight = 15619.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.117884 restraints weight = 21507.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.119014 restraints weight = 11645.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.119335 restraints weight = 8024.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.119825 restraints weight = 7669.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6218  Z= 0.271
  Angle     :  0.683   8.226   8592  Z= 0.362
  Chirality :  0.045   0.174   1087
  Planarity :  0.005   0.054   1152
  Dihedral  :  9.740 165.635   1067
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 26.71 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.28), residues: 1010
  helix:  2.63 (0.23), residues: 519
  sheet: -1.59 (0.39), residues: 169
  loop : -1.46 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  49 
 TYR   0.020   0.002   TYR B 145 
 PHE   0.029   0.003   PHE B 180 
 TRP   0.023   0.003   TRP B 297 
 HIS   0.009   0.003   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 6217)
  covalent geometry    : angle       0.68256 ( 8590)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       0.95357 (    2)
  hydrogen bonds       : bond        0.04293 (  450)
  hydrogen bonds       : angle       4.33724 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.227 
Fit side-chains
REVERT: B   93 ILE cc_start: 0.8113 (mm) cc_final: 0.7866 (mt)
REVERT: B  126 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5927 (tt)
  outliers start: 25
  outliers final: 17
  residues processed: 89
  average time/residue: 0.0615
  time to fit residues: 7.8671
Evaluate side-chains
  88 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:   30.0000
   chunk 42 optimal weight:    0.5980
   chunk 73 optimal weight:   60.0000
   chunk 91 optimal weight:   20.0000
   chunk 97 optimal weight:   30.0000
   chunk 17 optimal weight:   10.0000
   chunk 99 optimal weight:    0.0060
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    3.5202

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.140147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.106133 restraints weight = 15549.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.107480 restraints weight = 12997.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.108794 restraints weight = 9757.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.109193 restraints weight = 8861.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.109206 restraints weight = 8158.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6218  Z= 0.234
  Angle     :  0.651  10.037   8592  Z= 0.341
  Chirality :  0.044   0.171   1087
  Planarity :  0.005   0.056   1152
  Dihedral  :  9.810 169.552   1067
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.15 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 28.16 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.28), residues: 1010
  helix:  2.64 (0.23), residues: 516
  sheet: -1.60 (0.39), residues: 164
  loop : -1.71 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG A 256 
 TYR   0.019   0.002   TYR A 325 
 PHE   0.038   0.003   PHE B 292 
 TRP   0.019   0.003   TRP B 297 
 HIS   0.005   0.002   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 6217)
  covalent geometry    : angle       0.65104 ( 8590)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       0.87464 (    2)
  hydrogen bonds       : bond        0.04096 (  450)
  hydrogen bonds       : angle       4.24100 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (m-10)
REVERT: B   93 ILE cc_start: 0.8169 (mm) cc_final: 0.7890 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 90
  average time/residue: 0.0600
  time to fit residues: 7.6337
Evaluate side-chains
  93 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  339 PHE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 82 optimal weight:   20.0000
   chunk 90 optimal weight:    7.9990
   chunk 97 optimal weight:   30.0000
   chunk 21 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.142597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.108593 restraints weight = 15597.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.110660 restraints weight = 10812.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.112242 restraints weight = 8522.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.113042 restraints weight = 7310.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.113211 restraints weight = 6627.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6218  Z= 0.137
  Angle     :  0.584   9.755   8592  Z= 0.297
  Chirality :  0.041   0.153   1087
  Planarity :  0.004   0.050   1152
  Dihedral  :  9.579 173.106   1067
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 29.60 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.28), residues: 1010
  helix:  2.96 (0.22), residues: 520
  sheet: -1.53 (0.39), residues: 165
  loop : -1.52 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 256 
 TYR   0.009   0.001   TYR B 264 
 PHE   0.015   0.002   PHE B 292 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6217)
  covalent geometry    : angle       0.58435 ( 8590)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.49707 (    2)
  hydrogen bonds       : bond        0.03429 (  450)
  hydrogen bonds       : angle       3.91055 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6256 (t80)
REVERT: B   93 ILE cc_start: 0.8033 (mm) cc_final: 0.7766 (mt)
REVERT: G   44 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7436 (t-90)
  outliers start: 21
  outliers final: 15
  residues processed: 89
  average time/residue: 0.0673
  time to fit residues: 8.3234
Evaluate side-chains
  87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:   20.0000
   chunk 75 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    0.1980
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 51 optimal weight:    0.4980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.141426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.109700 restraints weight = 15583.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.109595 restraints weight = 11930.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.109747 restraints weight = 9930.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.110360 restraints weight = 10293.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.110516 restraints weight = 8942.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6218  Z= 0.166
  Angle     :  0.610   9.124   8592  Z= 0.312
  Chirality :  0.042   0.153   1087
  Planarity :  0.004   0.050   1152
  Dihedral  :  9.566 173.134   1067
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 29.60 %
    Favored  : 63.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.28), residues: 1010
  helix:  2.92 (0.22), residues: 519
  sheet: -1.47 (0.40), residues: 163
  loop : -1.60 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 256 
 TYR   0.014   0.002   TYR B  59 
 PHE   0.018   0.002   PHE B 180 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6217)
  covalent geometry    : angle       0.60953 ( 8590)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       0.57280 (    2)
  hydrogen bonds       : bond        0.03550 (  450)
  hydrogen bonds       : angle       3.94800 ( 1362)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  313 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6166 (t80)
REVERT: B   93 ILE cc_start: 0.8082 (mm) cc_final: 0.7807 (mt)
REVERT: G   44 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7668 (t-90)
  outliers start: 19
  outliers final: 15
  residues processed: 86
  average time/residue: 0.0636
  time to fit residues: 7.7367
Evaluate side-chains
  85 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 90 optimal weight:   30.0000
   chunk 57 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0050
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.144704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.121467 restraints weight = 15359.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.124790 restraints weight = 19181.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.125514 restraints weight = 9733.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.125910 restraints weight = 6946.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.126382 restraints weight = 6516.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   6218  Z= 0.109
  Angle     :  0.561   8.886   8592  Z= 0.283
  Chirality :  0.041   0.147   1087
  Planarity :  0.004   0.050   1152
  Dihedral  :  9.397 177.327   1067
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 32.13 %
    Favored  : 63.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.28), residues: 1010
  helix:  3.10 (0.22), residues: 521
  sheet: -1.31 (0.41), residues: 158
  loop : -1.52 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 256 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.015   0.001   PHE A 194 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6217)
  covalent geometry    : angle       0.56087 ( 8590)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.27338 (    2)
  hydrogen bonds       : bond        0.03088 (  450)
  hydrogen bonds       : angle       3.75274 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1092.66 seconds
wall clock time: 19 minutes 25.26 seconds (1165.26 seconds total)