Starting phenix.real_space_refine
on Sat Apr  4 22:01:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9odh_70359/04_2026/9odh_70359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9odh_70359/04_2026/9odh_70359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9odh_70359/04_2026/9odh_70359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9odh_70359/04_2026/9odh_70359.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9odh_70359/04_2026/9odh_70359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9odh_70359/04_2026/9odh_70359.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.036
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      17      5.16       5
     C    2789      2.51       5
     N     789      2.21       5
     O     797      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 4395
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2210
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 113}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 343
          Unresolved non-hydrogen angles: 426
          Unresolved non-hydrogen dihedrals: 262
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'ASP:plan': 25, 'GLN:plan1': 8, 'ARG:plan': 10, 'GLU:plan': 7, 'ASN:plan1': 6, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 211
    Chain: "C"
      Number of atoms: 309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 309
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 119
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 48
    Chain: "A"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 1844
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 195}
          Link IDs: {'PTRANS': 3, 'TRANS': 305}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 680
          Unresolved non-hydrogen angles: 838
          Unresolved non-hydrogen dihedrals: 544
          Unresolved non-hydrogen chiralities: 51
          Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 21, 'ARG:plan': 17, 'ASN:plan1': 13, 'TYR:plan': 4, 'GLN:plan1': 12, 'PHE:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 379
    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: 1.29, per 1000 atoms: 0.29
  Number of scatterers: 4395
  At special positions: 0
  Unit cell: (72.96, 97.92, 81.6, 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      17     16.00
     P       3     15.00
     O     797      8.00
     N     789      7.00
     C    2789      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.38
  Conformation dependent library (CDL) restraints added in 320.4 milliseconds
  

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1314

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 8 sheets defined
      33.6% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 3.895A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 25
      removed outlier: 3.651A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.726A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.922A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'A' and resid 9 through 30
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 3.999A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
    Processing helix  chain 'A' and resid 69 through 86
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 133 through 142
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 328 through 348
      removed outlier: 3.573A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 348 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.564A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.134A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.790A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.933A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192
      removed outlier: 7.140A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.624A  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: 6.262A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.680A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.595A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.323A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    657 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: 0.74

  Time building geometry restraints manager: 0.52 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: 1488
        1.34 -     1.46: 790
        1.46 -     1.57: 2171
        1.57 -     1.69: 5
        1.69 -     1.81: 23
  Bond restraints: 4477
  Sorted by residual:
  bond pdb=" C2  GTP A 401 "
       pdb=" N3  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.380  1.330  0.050 2.00e-02 2.50e+03 6.32e+00
  bond pdb=" CA  THR B  50 "
       pdb=" CB  THR B  50 "
    ideal  model  delta    sigma   weight residual
    1.531  1.562 -0.032 1.52e-02 4.33e+03 4.35e+00
  bond pdb=" C8  GTP A 401 "
       pdb=" N7  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.311  0.039 2.00e-02 2.50e+03 3.89e+00
  bond pdb=" C5  GTP A 401 "
       pdb=" N7  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.389 -0.039 2.00e-02 2.50e+03 3.72e+00
  bond pdb=" C4' GTP A 401 "
       pdb=" O4' GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.410  1.444 -0.034 2.00e-02 2.50e+03 2.86e+00
  ... (remaining 4472 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 6066
        2.12 -     4.25: 90
        4.25 -     6.37: 13
        6.37 -     8.50: 3
        8.50 -    10.62: 7
  Bond angle restraints: 6179
  Sorted by residual:
  angle pdb=" N   TRP A 211 "
        pdb=" CA  TRP A 211 "
        pdb=" C   TRP A 211 "
      ideal   model   delta    sigma   weight residual
     114.64  108.62    6.02 1.52e+00 4.33e-01 1.57e+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  100.38   10.62 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" O1B GTP A 401 "
        pdb=" PB  GTP A 401 "
        pdb=" O2B GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  119.79  -10.29 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" C2' GTP A 401 "
        pdb=" C3' GTP A 401 "
        pdb=" C4' GTP A 401 "
      ideal   model   delta    sigma   weight residual
     111.00  101.12    9.88 3.00e+00 1.11e-01 1.09e+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  129.76   -9.26 3.00e+00 1.11e-01 9.52e+00
  ... (remaining 6174 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.85: 2440
       27.85 -    55.69: 78
       55.69 -    83.54: 6
       83.54 -   111.39: 3
      111.39 -   139.23: 2
  Dihedral angle restraints: 2529
    sinusoidal: 512
      harmonic: 2017
  Sorted by residual:
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   70.31 -139.23     1      2.00e+01 2.50e-03 4.22e+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  -28.03  132.62     1      2.00e+01 2.50e-03 4.03e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21 -166.80  110.59     1      2.00e+01 2.50e-03 3.24e+01
  ... (remaining 2526 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 580
       0.043 -    0.086: 152
       0.086 -    0.129: 30
       0.129 -    0.172: 4
       0.172 -    0.216: 1
  Chirality restraints: 767
  Sorted by residual:
  chirality pdb=" C2' GTP A 401 "
            pdb=" C1' GTP A 401 "
            pdb=" C3' GTP A 401 "
            pdb=" O2' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.69    0.22 2.00e-01 2.50e+01 1.16e+00
  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   -2.64    0.17 2.00e-01 2.50e+01 7.31e-01
  chirality pdb=" CA  ASN B 110 "
            pdb=" N   ASN B 110 "
            pdb=" C   ASN B 110 "
            pdb=" CB  ASN B 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.31e-01
  ... (remaining 764 not shown)

  Planarity restraints: 800
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO B 236 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "   -0.016 2.00e-02 2.50e+03   9.45e-03 2.23e+00
        pdb=" CG  TRP B  82 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "   -0.022 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO C  49 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 797 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 913
        2.77 -     3.31: 3984
        3.31 -     3.84: 6794
        3.84 -     4.37: 6797
        4.37 -     4.90: 12855
  Nonbonded interactions: 31343
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ARG B  22 "
            pdb=" NE2 GLN B 259 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG  SER B 189 "
            pdb=" O   GLY B 202 "
     model   vdw
     2.349 3.040
  ... (remaining 31338 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:                  0.010
  Normalize map: mean=0, sd=1:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.380
  Find NCS groups from input model:        0.030
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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   0.078   4477  Z= 0.170
  Angle     :  0.753  10.619   6179  Z= 0.400
  Chirality :  0.040   0.216    767
  Planarity :  0.003   0.039    800
  Dihedral  : 15.638 139.233   1215
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.14 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 30.31 %
    Favored  : 68.50 %
  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:  0.00 (0.33), residues: 676
  helix:  2.71 (0.36), residues: 210
  sheet: -0.91 (0.37), residues: 173
  loop : -1.48 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.020   0.001   TYR A 296 
 PHE   0.007   0.001   PHE B 199 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4477)
  covalent geometry    : angle       0.75342 ( 6179)
  hydrogen bonds       : bond        0.15016 (  228)
  hydrogen bonds       : angle       5.56646 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.173 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 51
  average time/residue: 0.0451
  time to fit residues: 3.3340
Evaluate side-chains
  48 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
C  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.114481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.094595 restraints weight = 11142.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.096303 restraints weight = 7704.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.097495 restraints weight = 5934.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.098208 restraints weight = 4908.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098895 restraints weight = 4321.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4477  Z= 0.228
  Angle     :  0.593   6.447   6179  Z= 0.325
  Chirality :  0.042   0.144    767
  Planarity :  0.004   0.036    800
  Dihedral  :  9.920 128.906    732
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.40 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  8.27 %
    Allowed  : 25.59 %
    Favored  : 66.14 %
  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: -0.27 (0.32), residues: 676
  helix:  2.60 (0.36), residues: 202
  sheet: -1.07 (0.37), residues: 173
  loop : -1.62 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 150 
 TYR   0.015   0.002   TYR B 289 
 PHE   0.017   0.002   PHE B 199 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 4477)
  covalent geometry    : angle       0.59321 ( 6179)
  hydrogen bonds       : bond        0.04481 (  228)
  hydrogen bonds       : angle       5.00088 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.5515 (m-90)
REVERT: B  210 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8085 (tp)
REVERT: A   38 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8885 (mp)
  outliers start: 21
  outliers final: 11
  residues processed: 57
  average time/residue: 0.0430
  time to fit residues: 3.6360
Evaluate side-chains
  52 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.114697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.095510 restraints weight = 10960.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.096994 restraints weight = 8145.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.097264 restraints weight = 6043.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.097574 restraints weight = 5742.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.097659 restraints weight = 5257.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4477  Z= 0.190
  Angle     :  0.550   5.863   6179  Z= 0.302
  Chirality :  0.041   0.151    767
  Planarity :  0.003   0.035    800
  Dihedral  :  9.318 125.279    732
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.36 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  7.87 %
    Allowed  : 24.41 %
    Favored  : 67.72 %
  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: -0.26 (0.33), residues: 676
  helix:  2.54 (0.36), residues: 202
  sheet: -0.99 (0.38), residues: 178
  loop : -1.60 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 150 
 TYR   0.015   0.002   TYR A 154 
 PHE   0.015   0.002   PHE B 235 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4477)
  covalent geometry    : angle       0.55025 ( 6179)
  hydrogen bonds       : bond        0.04011 (  228)
  hydrogen bonds       : angle       4.73710 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8040 (OUTLIER) cc_final: 0.5780 (m-90)
REVERT: B  210 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7976 (tp)
REVERT: A   38 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8804 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 57
  average time/residue: 0.0455
  time to fit residues: 3.7359
Evaluate side-chains
  55 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0470
   chunk 32 optimal weight:    0.3980
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 39 optimal weight:   20.0000
   chunk 55 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 63 optimal weight:    0.9980
   overall best weight:    1.0880

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.117049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.096998 restraints weight = 10822.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.098640 restraints weight = 7705.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099784 restraints weight = 6052.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.100589 restraints weight = 5067.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.101017 restraints weight = 4469.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4477  Z= 0.120
  Angle     :  0.482   5.307   6179  Z= 0.261
  Chirality :  0.040   0.145    767
  Planarity :  0.003   0.035    800
  Dihedral  :  8.753 124.227    732
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 26.77 %
    Favored  : 66.54 %
  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: -0.10 (0.33), residues: 676
  helix:  2.62 (0.37), residues: 209
  sheet: -0.90 (0.38), residues: 178
  loop : -1.58 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.016   0.001   TYR A 154 
 PHE   0.009   0.001   PHE B 253 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4477)
  covalent geometry    : angle       0.48154 ( 6179)
  hydrogen bonds       : bond        0.03308 (  228)
  hydrogen bonds       : angle       4.31827 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.155 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7963 (OUTLIER) cc_final: 0.5630 (m-90)
REVERT: B  210 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7926 (tp)
REVERT: A   38 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8667 (mp)
  outliers start: 17
  outliers final: 13
  residues processed: 56
  average time/residue: 0.0408
  time to fit residues: 3.3131
Evaluate side-chains
  57 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  337 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 47 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0770
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.3744

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.116064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.095961 restraints weight = 10954.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.097592 restraints weight = 7773.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098792 restraints weight = 6063.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.099616 restraints weight = 5072.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.099942 restraints weight = 4454.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4477  Z= 0.142
  Angle     :  0.495   5.682   6179  Z= 0.271
  Chirality :  0.040   0.156    767
  Planarity :  0.003   0.033    800
  Dihedral  :  8.528 120.250    732
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  9.84 %
    Allowed  : 24.80 %
    Favored  : 65.35 %
  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: -0.07 (0.33), residues: 676
  helix:  2.65 (0.36), residues: 209
  sheet: -0.85 (0.39), residues: 173
  loop : -1.57 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.016   0.002   TYR A 154 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4477)
  covalent geometry    : angle       0.49477 ( 6179)
  hydrogen bonds       : bond        0.03459 (  228)
  hydrogen bonds       : angle       4.26409 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 40
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.5720 (m-90)
REVERT: B  210 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7949 (tp)
REVERT: A   38 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8765 (mp)
  outliers start: 25
  outliers final: 20
  residues processed: 62
  average time/residue: 0.0438
  time to fit residues: 3.9710
Evaluate side-chains
  63 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 40
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  337 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.118480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.098405 restraints weight = 10939.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.100115 restraints weight = 7726.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.101223 restraints weight = 6000.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.102108 restraints weight = 5017.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.102598 restraints weight = 4397.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4477  Z= 0.097
  Angle     :  0.462   5.803   6179  Z= 0.249
  Chirality :  0.040   0.152    767
  Planarity :  0.003   0.033    800
  Dihedral  :  7.909 116.587    732
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  8.66 %
    Allowed  : 26.77 %
    Favored  : 64.57 %
  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:  0.08 (0.34), residues: 676
  helix:  2.88 (0.36), residues: 209
  sheet: -0.70 (0.39), residues: 173
  loop : -1.63 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.017   0.001   TYR A 154 
 PHE   0.008   0.001   PHE B 253 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 4477)
  covalent geometry    : angle       0.46203 ( 6179)
  hydrogen bonds       : bond        0.02938 (  228)
  hydrogen bonds       : angle       4.01003 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.097 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.5640 (m-90)
REVERT: B  210 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7914 (tp)
REVERT: A   38 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: A  131 TRP cc_start: 0.8730 (t60) cc_final: 0.8431 (t60)
  outliers start: 22
  outliers final: 17
  residues processed: 61
  average time/residue: 0.0393
  time to fit residues: 3.5062
Evaluate side-chains
  61 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  337 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.115814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.095842 restraints weight = 10931.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.097453 restraints weight = 7779.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.098582 restraints weight = 6067.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.099016 restraints weight = 5088.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.099813 restraints weight = 4618.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4477  Z= 0.172
  Angle     :  0.527   6.680   6179  Z= 0.285
  Chirality :  0.041   0.155    767
  Planarity :  0.003   0.032    800
  Dihedral  :  7.885 115.238    732
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  9.45 %
    Allowed  : 26.38 %
    Favored  : 64.17 %
  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: -0.10 (0.34), residues: 676
  helix:  2.84 (0.36), residues: 203
  sheet: -1.01 (0.38), residues: 180
  loop : -1.58 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.017   0.002   TYR A 154 
 PHE   0.015   0.002   PHE B 241 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 4477)
  covalent geometry    : angle       0.52704 ( 6179)
  hydrogen bonds       : bond        0.03607 (  228)
  hydrogen bonds       : angle       4.26430 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 38
  time to evaluate  : 0.154 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.5732 (m-90)
REVERT: B  210 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7971 (tp)
REVERT: A   38 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8842 (mp)
  outliers start: 24
  outliers final: 20
  residues processed: 59
  average time/residue: 0.0390
  time to fit residues: 3.5917
Evaluate side-chains
  60 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 37
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  337 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0270
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 54 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0870
   chunk 39 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.3216

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.121079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.101276 restraints weight = 10877.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.102953 restraints weight = 7637.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.104222 restraints weight = 5915.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.104913 restraints weight = 4903.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.105703 restraints weight = 4321.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4477  Z= 0.078
  Angle     :  0.458   6.779   6179  Z= 0.240
  Chirality :  0.039   0.144    767
  Planarity :  0.003   0.032    800
  Dihedral  :  6.893 105.478    732
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  7.87 %
    Allowed  : 28.74 %
    Favored  : 63.39 %
  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:  0.21 (0.34), residues: 676
  helix:  3.07 (0.36), residues: 209
  sheet: -0.69 (0.39), residues: 176
  loop : -1.58 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 219 
 TYR   0.018   0.001   TYR A 154 
 PHE   0.005   0.001   PHE B 335 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00164 ( 4477)
  covalent geometry    : angle       0.45798 ( 6179)
  hydrogen bonds       : bond        0.02600 (  228)
  hydrogen bonds       : angle       3.82142 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.156 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.5562 (m-90)
REVERT: B  210 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7822 (tp)
REVERT: A   38 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8426 (mp)
REVERT: A  131 TRP cc_start: 0.8626 (t60) cc_final: 0.8383 (t60)
  outliers start: 20
  outliers final: 17
  residues processed: 62
  average time/residue: 0.0424
  time to fit residues: 3.8146
Evaluate side-chains
  62 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 38 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 12 optimal weight:    0.3980
   chunk 53 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.118821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.098949 restraints weight = 10732.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.100549 restraints weight = 7578.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.101724 restraints weight = 5928.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.102429 restraints weight = 4940.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.102903 restraints weight = 4361.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4477  Z= 0.107
  Angle     :  0.486   8.660   6179  Z= 0.255
  Chirality :  0.040   0.151    767
  Planarity :  0.003   0.033    800
  Dihedral  :  6.664  96.922    732
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  8.27 %
    Allowed  : 29.13 %
    Favored  : 62.60 %
  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:  0.21 (0.34), residues: 676
  helix:  3.03 (0.36), residues: 209
  sheet: -0.65 (0.39), residues: 175
  loop : -1.58 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.017   0.002   TYR A 154 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 4477)
  covalent geometry    : angle       0.48557 ( 6179)
  hydrogen bonds       : bond        0.03005 (  228)
  hydrogen bonds       : angle       3.83496 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 41
  time to evaluate  : 0.155 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.5646 (m-90)
REVERT: B  210 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7930 (tp)
REVERT: A   38 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8667 (mp)
REVERT: A  131 TRP cc_start: 0.8636 (t60) cc_final: 0.8412 (t60)
  outliers start: 21
  outliers final: 16
  residues processed: 58
  average time/residue: 0.0483
  time to fit residues: 3.9510
Evaluate side-chains
  59 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 46 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0670
   chunk 3 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.4722

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.117139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.096837 restraints weight = 10897.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.098478 restraints weight = 7776.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.099564 restraints weight = 6096.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.100147 restraints weight = 5124.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100923 restraints weight = 4582.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4477  Z= 0.149
  Angle     :  0.520   8.286   6179  Z= 0.276
  Chirality :  0.040   0.156    767
  Planarity :  0.003   0.033    800
  Dihedral  :  6.746  95.260    732
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  8.66 %
    Allowed  : 29.53 %
    Favored  : 61.81 %
  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:  0.02 (0.34), residues: 676
  helix:  2.87 (0.36), residues: 209
  sheet: -0.96 (0.38), residues: 182
  loop : -1.53 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.018   0.002   TYR A 154 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4477)
  covalent geometry    : angle       0.52026 ( 6179)
  hydrogen bonds       : bond        0.03393 (  228)
  hydrogen bonds       : angle       4.07234 (  657)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 38
  time to evaluate  : 0.156 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.7968 (OUTLIER) cc_final: 0.5733 (m-90)
REVERT: B  210 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7952 (tp)
REVERT: A   38 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8814 (mp)
REVERT: A  131 TRP cc_start: 0.8657 (t60) cc_final: 0.8428 (t60)
  outliers start: 22
  outliers final: 18
  residues processed: 57
  average time/residue: 0.0297
  time to fit residues: 2.6819
Evaluate side-chains
  59 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 13 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.118699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.098751 restraints weight = 10938.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.100416 restraints weight = 7738.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.101559 restraints weight = 6025.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.102428 restraints weight = 5034.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.102919 restraints weight = 4405.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4477  Z= 0.093
  Angle     :  0.475   8.034   6179  Z= 0.248
  Chirality :  0.039   0.148    767
  Planarity :  0.003   0.033    800
  Dihedral  :  6.297  91.823    732
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  8.27 %
    Allowed  : 30.31 %
    Favored  : 61.42 %
  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:  0.20 (0.34), residues: 676
  helix:  3.06 (0.36), residues: 209
  sheet: -0.67 (0.39), residues: 175
  loop : -1.61 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.018   0.001   TYR A 154 
 PHE   0.007   0.001   PHE B 253 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 4477)
  covalent geometry    : angle       0.47481 ( 6179)
  hydrogen bonds       : bond        0.02833 (  228)
  hydrogen bonds       : angle       3.84450 (  657)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 825.22 seconds
wall clock time: 14 minutes 46.91 seconds (886.91 seconds total)