Starting phenix.real_space_refine
on Sat Apr  4 23:19:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p83_71363/04_2026/9p83_71363.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p83_71363/04_2026/9p83_71363.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p83_71363/04_2026/9p83_71363.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p83_71363/04_2026/9p83_71363.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p83_71363/04_2026/9p83_71363.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p83_71363/04_2026/9p83_71363.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
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      19      5.16       5
     C    3610      2.51       5
     N    1010      2.21       5
     O    1019      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  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: 5661
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 1713
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 150}
          Link IDs: {'PTRANS': 10, 'TRANS': 266}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 536
          Unresolved non-hydrogen angles: 695
          Unresolved non-hydrogen dihedrals: 447
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'TYR:plan': 6, 'PHE:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 11, 'GLN:plan1': 4, 'HIS:plan': 7, 'GLU:plan': 4, 'TRP:plan': 3, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 266
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 1395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1395
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 106}
          Link IDs: {'PTRANS': 1, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 335
          Unresolved non-hydrogen angles: 410
          Unresolved non-hydrogen dihedrals: 268
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 12, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 155
    Chain: "B"
      Number of atoms: 2167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2167
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 403
          Unresolved non-hydrogen angles: 504
          Unresolved non-hydrogen dihedrals: 304
          Unresolved non-hydrogen chiralities: 37
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 23, 'GLN:plan1': 8, 'ARG:plan': 15, 'ASN:plan1': 8, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 236
    Chain: "C"
      Number of atoms: 296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 296
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 53
    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: 1.44, per 1000 atoms: 0.25
  Number of scatterers: 5661
  At special positions: 0
  Unit cell: (82.368, 96.512, 119.808, 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      19     16.00
     P       3     15.00
     O    1019      8.00
     N    1010      7.00
     C    3610      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: 0.40
  Conformation dependent library (CDL) restraints added in 358.7 milliseconds
  

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1678

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      48.8% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 59 through 90
    Processing helix  chain 'R' and resid 98 through 116
    Processing helix  chain 'R' and resid 119 through 126
    Processing helix  chain 'R' and resid 137 through 172
      removed outlier: 3.976A  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 200
      removed outlier: 3.512A  pdb=" N   ALA R 200 " --> pdb=" O   SER R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 200 through 207
      removed outlier: 3.684A  pdb=" N   MET R 207 " --> pdb=" O   MET R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 244
    Processing helix  chain 'R' and resid 245 through 269
      removed outlier: 4.070A  pdb=" N   THR R 257 " --> pdb=" O   SER R 253 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 292 through 329
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 356
    Processing helix  chain 'R' and resid 359 through 368
    Processing helix  chain 'R' and resid 368 through 373
      removed outlier: 3.802A  pdb=" N   ARG R 372 " --> pdb=" O   SER R 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 33
      removed outlier: 3.724A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.204A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.584A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 311
      removed outlier: 3.778A  pdb=" N   ASN A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.923A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.548A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.682A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR A 320 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.642A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.751A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 151
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.813A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.914A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 277
      removed outlier: 6.647A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320
      removed outlier: 3.746A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1146 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: 0.89

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1918
        1.34 -     1.46: 1351
        1.46 -     1.58: 2474
        1.58 -     1.70: 5
        1.70 -     1.82: 23
  Bond restraints: 5771
  Sorted by residual:
  bond pdb=" N   ARG L   9 "
       pdb=" CA  ARG L   9 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.60e-02 3.91e+03 3.24e+00
  bond pdb=" N   ARG L   8 "
       pdb=" CA  ARG L   8 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.57e+00
  bond pdb=" C   ARG L   9 "
       pdb=" N   PRO L  10 "
    ideal  model  delta    sigma   weight residual
    1.332  1.350 -0.018 1.34e-02 5.57e+03 1.75e+00
  bond pdb=" CG  LEU B 285 "
       pdb=" CD2 LEU B 285 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" CA  ILE C  25 "
       pdb=" CB  ILE C  25 "
    ideal  model  delta    sigma   weight residual
    1.550  1.540  0.010 1.03e-02 9.43e+03 1.02e+00
  ... (remaining 5766 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 7796
        1.86 -     3.71: 130
        3.71 -     5.57: 21
        5.57 -     7.42: 4
        7.42 -     9.28: 2
  Bond angle restraints: 7953
  Sorted by residual:
  angle pdb=" N   ASP B  27 "
        pdb=" CA  ASP B  27 "
        pdb=" C   ASP B  27 "
      ideal   model   delta    sigma   weight residual
     112.72  108.29    4.43 1.28e+00 6.10e-01 1.20e+01
  angle pdb=" N   MET A 247 "
        pdb=" CA  MET A 247 "
        pdb=" CB  MET A 247 "
      ideal   model   delta    sigma   weight residual
     110.39  115.85   -5.46 1.66e+00 3.63e-01 1.08e+01
  angle pdb=" C   ASN A 269 "
        pdb=" CA  ASN A 269 "
        pdb=" CB  ASN A 269 "
      ideal   model   delta    sigma   weight residual
     109.80  115.12   -5.32 1.65e+00 3.67e-01 1.04e+01
  angle pdb=" N   VAL R 130 "
        pdb=" CA  VAL R 130 "
        pdb=" C   VAL R 130 "
      ideal   model   delta    sigma   weight residual
     106.21  109.50   -3.29 1.07e+00 8.73e-01 9.48e+00
  angle pdb=" CA  LEU B 300 "
        pdb=" CB  LEU B 300 "
        pdb=" CG  LEU B 300 "
      ideal   model   delta    sigma   weight residual
     116.30  125.58   -9.28 3.50e+00 8.16e-02 7.03e+00
  ... (remaining 7948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.17: 3161
       27.17 -    54.33: 108
       54.33 -    81.50: 10
       81.50 -   108.66: 1
      108.66 -   135.83: 2
  Dihedral angle restraints: 3282
    sinusoidal: 707
      harmonic: 2575
  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
      93.00  155.73  -62.73     1      1.00e+01 1.00e-02 5.20e+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  -31.23  135.83     1      2.00e+01 2.50e-03 4.12e+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
     274.12  161.50  112.62     1      2.00e+01 2.50e-03 3.32e+01
  ... (remaining 3279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 670
       0.037 -    0.075: 206
       0.075 -    0.112: 76
       0.112 -    0.150: 11
       0.150 -    0.187: 5
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" CB  THR R 349 "
            pdb=" CA  THR R 349 "
            pdb=" OG1 THR R 349 "
            pdb=" CG2 THR R 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.77e-01
  chirality pdb=" CB  THR R 152 "
            pdb=" CA  THR R 152 "
            pdb=" OG1 THR R 152 "
            pdb=" CG2 THR R 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.19e-01
  chirality pdb=" CA  MET A 247 "
            pdb=" N   MET A 247 "
            pdb=" C   MET A 247 "
            pdb=" CB  MET A 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 965 not shown)

  Planarity restraints: 1043
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   9 "    0.273 9.50e-02 1.11e+02   1.22e-01 9.21e+00
        pdb=" NE  ARG L   9 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   9 "    0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   9 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  76 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" CG  ASP B  76 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  76 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  76 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO B 236 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1040 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 164
        2.71 -     3.26: 5723
        3.26 -     3.81: 9358
        3.81 -     4.35: 10339
        4.35 -     4.90: 18519
  Nonbonded interactions: 44103
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" N   LYS A 270 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   HIS R 131 "
            pdb=" OH  TYR L  11 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG  SER R 107 "
            pdb=" OD1 ASN R 158 "
     model   vdw
     2.316 3.040
  ... (remaining 44098 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.740
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
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      :  0.003   0.039   5772  Z= 0.168
  Angle     :  0.646   9.279   7955  Z= 0.372
  Chirality :  0.043   0.187    968
  Planarity :  0.005   0.122   1043
  Dihedral  : 14.558 135.827   1601
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.30 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 25.30 %
    Favored  : 74.40 %
  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:  0.93 (0.31), residues: 861
  helix:  2.42 (0.26), residues: 417
  sheet: -1.57 (0.38), residues: 175
  loop : -0.67 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L   9 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.025   0.002   PHE R 353 
 TRP   0.028   0.002   TRP B 339 
 HIS   0.014   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5771)
  covalent geometry    : angle       0.64553 ( 7953)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       1.00093 (    2)
  hydrogen bonds       : bond        0.12331 (  398)
  hydrogen bonds       : angle       5.16730 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 0.0411
  time to fit residues: 5.2342
Evaluate side-chains
  84 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** R 320 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 = 0.4547 r_free = 0.4547 target = 0.209320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.170409 restraints weight = 8023.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 2.52
r_work: 0.3917 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3794 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.0952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5772  Z= 0.168
  Angle     :  0.552   8.586   7955  Z= 0.291
  Chirality :  0.043   0.148    968
  Planarity :  0.004   0.049   1043
  Dihedral  :  8.884 136.806    929
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.07 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.89 %
    Favored  : 73.19 %
  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:  1.07 (0.30), residues: 861
  helix:  2.76 (0.25), residues: 411
  sheet: -1.52 (0.37), residues: 174
  loop : -0.92 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L   9 
 TYR   0.012   0.001   TYR R 364 
 PHE   0.017   0.002   PHE B 235 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5771)
  covalent geometry    : angle       0.55153 ( 7953)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       1.09779 (    2)
  hydrogen bonds       : bond        0.04074 (  398)
  hydrogen bonds       : angle       4.38035 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: R  204 LEU cc_start: 0.8128 (tp) cc_final: 0.7832 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0484
  time to fit residues: 7.0948
Evaluate side-chains
  92 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:   20.0000
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4525 r_free = 0.4525 target = 0.206527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.168530 restraints weight = 7897.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 2.40
r_work: 0.3891 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5772  Z= 0.198
  Angle     :  0.579   8.482   7955  Z= 0.307
  Chirality :  0.045   0.158    968
  Planarity :  0.004   0.054   1043
  Dihedral  :  8.911 137.653    929
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.41 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 21.39 %
    Favored  : 71.39 %
  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:  1.04 (0.30), residues: 861
  helix:  2.87 (0.25), residues: 399
  sheet: -1.52 (0.36), residues: 176
  loop : -1.01 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 208 
 TYR   0.010   0.001   TYR R 364 
 PHE   0.025   0.002   PHE B 235 
 TRP   0.030   0.002   TRP B 339 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 5771)
  covalent geometry    : angle       0.57852 ( 7953)
  SS BOND              : bond        0.00144 (    1)
  SS BOND              : angle       1.21539 (    2)
  hydrogen bonds       : bond        0.04210 (  398)
  hydrogen bonds       : angle       4.41261 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: R  204 LEU cc_start: 0.8139 (tp) cc_final: 0.7922 (mt)
REVERT: B  188 MET cc_start: 0.7861 (mmm) cc_final: 0.7647 (mmp)
REVERT: B  286 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7186 (mt)
  outliers start: 24
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0434
  time to fit residues: 6.7657
Evaluate side-chains
  102 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  317 LEU
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:   40.0000
   chunk 37 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 48 optimal weight:    0.3980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4568 r_free = 0.4568 target = 0.211043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.172414 restraints weight = 7909.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 2.42
r_work: 0.3956 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5772  Z= 0.112
  Angle     :  0.498   7.541   7955  Z= 0.258
  Chirality :  0.042   0.147    968
  Planarity :  0.003   0.049   1043
  Dihedral  :  8.495 132.614    929
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.79 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 22.89 %
    Favored  : 71.69 %
  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:  1.32 (0.30), residues: 861
  helix:  3.05 (0.25), residues: 406
  sheet: -1.33 (0.36), residues: 174
  loop : -0.95 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 313 
 TYR   0.009   0.001   TYR R 364 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.024   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5771)
  covalent geometry    : angle       0.49744 ( 7953)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       0.71479 (    2)
  hydrogen bonds       : bond        0.03304 (  398)
  hydrogen bonds       : angle       3.98774 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0495
  time to fit residues: 7.5685
Evaluate side-chains
  100 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  292 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0870
   chunk 50 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.8162

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4561 r_free = 0.4561 target = 0.210290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.171728 restraints weight = 8112.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 2.56
r_work: 0.3928 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5772  Z= 0.121
  Angle     :  0.509   8.454   7955  Z= 0.263
  Chirality :  0.042   0.142    968
  Planarity :  0.003   0.049   1043
  Dihedral  :  8.441 135.635    929
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.48 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 22.89 %
    Favored  : 69.88 %
  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:  1.42 (0.30), residues: 861
  helix:  3.16 (0.25), residues: 406
  sheet: -1.34 (0.36), residues: 174
  loop : -0.90 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.008   0.001   TYR R 364 
 PHE   0.018   0.001   PHE R 353 
 TRP   0.025   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5771)
  covalent geometry    : angle       0.50844 ( 7953)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.77470 (    2)
  hydrogen bonds       : bond        0.03320 (  398)
  hydrogen bonds       : angle       3.91868 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: R  345 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6030 (t80)
REVERT: B  286 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7112 (mt)
  outliers start: 24
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0455
  time to fit residues: 7.1609
Evaluate side-chains
  107 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  144 TYR
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  317 LEU
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain R residue  345 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4552 r_free = 0.4552 target = 0.209410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.170286 restraints weight = 8006.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 2.57
r_work: 0.3956 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5772  Z= 0.137
  Angle     :  0.529   8.553   7955  Z= 0.274
  Chirality :  0.043   0.164    968
  Planarity :  0.003   0.051   1043
  Dihedral  :  8.415 133.611    929
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.72 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  7.83 %
    Allowed  : 23.19 %
    Favored  : 68.98 %
  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:  1.48 (0.30), residues: 861
  helix:  3.24 (0.25), residues: 406
  sheet: -1.31 (0.36), residues: 171
  loop : -0.93 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.007   0.001   TYR B 105 
 PHE   0.016   0.002   PHE A 334 
 TRP   0.032   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5771)
  covalent geometry    : angle       0.52895 ( 7953)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.89386 (    2)
  hydrogen bonds       : bond        0.03393 (  398)
  hydrogen bonds       : angle       3.93433 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: R  345 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6228 (t80)
REVERT: B  286 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7264 (mt)
REVERT: B  336 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7874 (mp)
  outliers start: 26
  outliers final: 21
  residues processed: 106
  average time/residue: 0.0477
  time to fit residues: 7.4024
Evaluate side-chains
  109 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  144 TYR
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  317 LEU
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain R residue  345 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0170
   chunk 75 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 6 optimal weight:   20.0000
   chunk 73 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.8224

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4565 r_free = 0.4565 target = 0.210725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.171430 restraints weight = 8091.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 2.61
r_work: 0.3980 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3859 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5772  Z= 0.118
  Angle     :  0.509   8.018   7955  Z= 0.263
  Chirality :  0.042   0.145    968
  Planarity :  0.003   0.050   1043
  Dihedral  :  8.213 130.767    929
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.25 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  7.83 %
    Allowed  : 23.80 %
    Favored  : 68.37 %
  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:  1.59 (0.31), residues: 861
  helix:  3.33 (0.25), residues: 406
  sheet: -1.25 (0.37), residues: 174
  loop : -0.86 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.007   0.001   TYR R 364 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.028   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5771)
  covalent geometry    : angle       0.50855 ( 7953)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       0.65230 (    2)
  hydrogen bonds       : bond        0.03190 (  398)
  hydrogen bonds       : angle       3.85923 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: R  345 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6236 (t80)
REVERT: B  286 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7234 (mt)
REVERT: B  336 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7920 (mp)
  outliers start: 26
  outliers final: 21
  residues processed: 105
  average time/residue: 0.0400
  time to fit residues: 6.4042
Evaluate side-chains
  109 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  144 TYR
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  317 LEU
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain R residue  345 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:   30.0000
   chunk 71 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.211298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.168564 restraints weight = 7972.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 3.29
r_work: 0.3964 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5772  Z= 0.116
  Angle     :  0.514   9.360   7955  Z= 0.263
  Chirality :  0.042   0.157    968
  Planarity :  0.003   0.050   1043
  Dihedral  :  8.041 127.798    929
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.90 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 24.70 %
    Favored  : 68.07 %
  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:  1.66 (0.31), residues: 861
  helix:  3.39 (0.25), residues: 406
  sheet: -1.20 (0.37), residues: 174
  loop : -0.84 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 208 
 TYR   0.006   0.001   TYR R 319 
 PHE   0.017   0.001   PHE A 336 
 TRP   0.028   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5771)
  covalent geometry    : angle       0.51406 ( 7953)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.64383 (    2)
  hydrogen bonds       : bond        0.03152 (  398)
  hydrogen bonds       : angle       3.79109 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: R  345 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6125 (t80)
REVERT: B  286 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7029 (mt)
REVERT: B  336 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7837 (mp)
  outliers start: 24
  outliers final: 21
  residues processed: 105
  average time/residue: 0.0433
  time to fit residues: 6.8937
Evaluate side-chains
  109 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  144 TYR
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  317 LEU
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain R residue  345 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0020
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4597 r_free = 0.4597 target = 0.213300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.173164 restraints weight = 7930.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 2.40
r_work: 0.4017 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3901 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5772  Z= 0.109
  Angle     :  0.517   9.372   7955  Z= 0.262
  Chirality :  0.042   0.154    968
  Planarity :  0.003   0.050   1043
  Dihedral  :  7.870 126.956    929
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.67 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 25.60 %
    Favored  : 67.77 %
  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:  1.70 (0.31), residues: 861
  helix:  3.39 (0.25), residues: 407
  sheet: -1.18 (0.37), residues: 174
  loop : -0.80 (0.40), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L   9 
 TYR   0.006   0.001   TYR R 364 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.025   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5771)
  covalent geometry    : angle       0.51728 ( 7953)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       0.53670 (    2)
  hydrogen bonds       : bond        0.03032 (  398)
  hydrogen bonds       : angle       3.75524 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: R  345 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6263 (t80)
REVERT: B  286 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7124 (mt)
REVERT: B  336 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7890 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 101
  average time/residue: 0.0380
  time to fit residues: 5.8412
Evaluate side-chains
  105 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  144 TYR
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain R residue  345 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 84 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 16 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4592 r_free = 0.4592 target = 0.212976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.172535 restraints weight = 8026.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 2.40
r_work: 0.4003 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3889 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5772  Z= 0.115
  Angle     :  0.530   9.602   7955  Z= 0.267
  Chirality :  0.042   0.164    968
  Planarity :  0.003   0.050   1043
  Dihedral  :  7.694 123.833    929
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.48 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 26.81 %
    Favored  : 67.47 %
  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:  1.70 (0.31), residues: 861
  helix:  3.40 (0.25), residues: 407
  sheet: -1.32 (0.36), residues: 179
  loop : -0.69 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 208 
 TYR   0.006   0.001   TYR R 339 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.021   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5771)
  covalent geometry    : angle       0.53038 ( 7953)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.59707 (    2)
  hydrogen bonds       : bond        0.03071 (  398)
  hydrogen bonds       : angle       3.73261 ( 1146)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: R  345 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6250 (t80)
REVERT: B  286 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7135 (mt)
REVERT: B  336 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7847 (mp)
  outliers start: 19
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0460
  time to fit residues: 6.9870
Evaluate side-chains
  107 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  144 TYR
Chi-restraints excluded: chain R residue  224 CYS
Chi-restraints excluded: chain R residue  321 VAL
Chi-restraints excluded: chain R residue  345 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 320 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 = 0.4557 r_free = 0.4557 target = 0.209042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.168339 restraints weight = 7863.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 2.49
r_work: 0.3951 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3834 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5772  Z= 0.173
  Angle     :  0.584   8.868   7955  Z= 0.299
  Chirality :  0.044   0.163    968
  Planarity :  0.003   0.054   1043
  Dihedral  :  7.825 123.009    929
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.83 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 25.60 %
    Favored  : 67.77 %
  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:  1.56 (0.31), residues: 861
  helix:  3.28 (0.25), residues: 407
  sheet: -1.35 (0.37), residues: 176
  loop : -0.78 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.012   0.001   TYR B 105 
 PHE   0.020   0.002   PHE B 235 
 TRP   0.037   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5771)
  covalent geometry    : angle       0.58418 ( 7953)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.97423 (    2)
  hydrogen bonds       : bond        0.03643 (  398)
  hydrogen bonds       : angle       4.00252 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1735.13 seconds
wall clock time: 30 minutes 12.90 seconds (1812.90 seconds total)