Starting phenix.real_space_refine
on Thu Mar  6 06:04:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n0k_24107/03_2025/7n0k_24107.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n0k_24107/03_2025/7n0k_24107.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n0k_24107/03_2025/7n0k_24107.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n0k_24107/03_2025/7n0k_24107.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n0k_24107/03_2025/7n0k_24107.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n0k_24107/03_2025/7n0k_24107.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3404      2.51       5
     N     852      2.21       5
     O     868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5154
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2577
          Classifications: {'peptide': 313}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 6, 'TRANS': 306}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.57, per 1000 atoms: 0.89
  Number of scatterers: 5154
  At special positions: 0
  Unit cell: (97.85, 91.67, 90.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     868      8.00
     N     852      7.00
     C    3404      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: 1.38
  Conformation dependent library (CDL) restraints added in 692.9 milliseconds
  

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1188

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      88.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 68
      removed outlier: 4.273A  pdb=" N   TRP B  16 " --> pdb=" O   CYS B  12 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLU B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP B  18 " --> pdb=" O   ARG B  14 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY B  25 " --> pdb=" O   GLN B  21 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU B  35 " --> pdb=" O   ARG B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 101
      removed outlier: 3.907A  pdb=" N   ALA B  99 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   TYR B 100 " --> pdb=" O   ASP B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 112
    Processing helix  chain 'B' and resid 122 through 154
      removed outlier: 3.832A  pdb=" N   LYS B 130 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE B 143 " --> pdb=" O   TYR B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 186
      removed outlier: 3.698A  pdb=" N   ILE B 177 " --> pdb=" O   CYS B 173 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 182 " --> pdb=" O   ARG B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 209
      removed outlier: 4.079A  pdb=" N   VAL B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   PHE B 195 " --> pdb=" O   GLY B 191 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR B 198 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR B 201 " --> pdb=" O   HIS B 197 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B 208 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR B 209 " --> pdb=" O   GLY B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 219
      removed outlier: 3.585A  pdb=" N   LYS B 218 " --> pdb=" O   MET B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 250
      removed outlier: 3.968A  pdb=" N   PHE B 226 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY B 243 " --> pdb=" O   TYR B 239 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG B 247 " --> pdb=" O   GLY B 243 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA B 250 " --> pdb=" O   TYR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 298
      Proline residue:  B 277  - end of helix
    Processing helix  chain 'B' and resid 305 through 335
      removed outlier: 3.857A  pdb=" N   MET B 309 " --> pdb=" O   TRP B 305 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      Proline residue:  B 313  - end of helix
      removed outlier: 3.585A  pdb=" N   PHE B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 68
      removed outlier: 4.273A  pdb=" N   TRP A  16 " --> pdb=" O   CYS A  12 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ASP A  18 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 101
      removed outlier: 3.906A  pdb=" N   ALA A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   TYR A 100 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 112
    Processing helix  chain 'A' and resid 122 through 154
      removed outlier: 3.832A  pdb=" N   LYS A 130 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ILE A 143 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 186
      removed outlier: 3.699A  pdb=" N   ILE A 177 " --> pdb=" O   CYS A 173 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LEU A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 209
      removed outlier: 4.078A  pdb=" N   VAL A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   PHE A 195 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   TYR A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR A 201 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 208 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 209 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 219
      removed outlier: 3.585A  pdb=" N   LYS A 218 " --> pdb=" O   MET A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 250
      removed outlier: 3.967A  pdb=" N   PHE A 226 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY A 243 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 298
      Proline residue:  A 277  - end of helix
    Processing helix  chain 'A' and resid 305 through 335
      removed outlier: 3.858A  pdb=" N   MET A 309 " --> pdb=" O   TRP A 305 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
      removed outlier: 3.584A  pdb=" N   PHE A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1215 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1576
        1.34 -     1.46: 1379
        1.46 -     1.58: 2297
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 5296
  Sorted by residual:
  bond pdb=" CB  GLN B 124 "
       pdb=" CG  GLN B 124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" CB  GLN A 124 "
       pdb=" CG  GLN A 124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.25e+00
  bond pdb=" C   TRP A 210 "
       pdb=" N   PRO A 211 "
    ideal  model  delta    sigma   weight residual
    1.333  1.323  0.010 1.20e-02 6.94e+03 7.61e-01
  bond pdb=" C   TRP B 210 "
       pdb=" N   PRO B 211 "
    ideal  model  delta    sigma   weight residual
    1.333  1.323  0.010 1.20e-02 6.94e+03 7.52e-01
  bond pdb=" N   GLY A 213 "
       pdb=" CA  GLY A 213 "
    ideal  model  delta    sigma   weight residual
    1.455  1.447  0.008 1.05e-02 9.07e+03 5.51e-01
  ... (remaining 5291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 7005
        1.53 -     3.07: 133
        3.07 -     4.60: 18
        4.60 -     6.14: 4
        6.14 -     7.67: 4
  Bond angle restraints: 7164
  Sorted by residual:
  angle pdb=" CA  GLN B 124 "
        pdb=" CB  GLN B 124 "
        pdb=" CG  GLN B 124 "
      ideal   model   delta    sigma   weight residual
     114.10  121.77   -7.67 2.00e+00 2.50e-01 1.47e+01
  angle pdb=" CA  GLN A 124 "
        pdb=" CB  GLN A 124 "
        pdb=" CG  GLN A 124 "
      ideal   model   delta    sigma   weight residual
     114.10  121.74   -7.64 2.00e+00 2.50e-01 1.46e+01
  angle pdb=" CB  GLN A 124 "
        pdb=" CG  GLN A 124 "
        pdb=" CD  GLN A 124 "
      ideal   model   delta    sigma   weight residual
     112.60  116.00   -3.40 1.70e+00 3.46e-01 3.99e+00
  angle pdb=" CB  GLN B 124 "
        pdb=" CG  GLN B 124 "
        pdb=" CD  GLN B 124 "
      ideal   model   delta    sigma   weight residual
     112.60  115.97   -3.37 1.70e+00 3.46e-01 3.93e+00
  angle pdb=" CA  LEU A 120 "
        pdb=" CB  LEU A 120 "
        pdb=" CG  LEU A 120 "
      ideal   model   delta    sigma   weight residual
     116.30  122.71   -6.41 3.50e+00 8.16e-02 3.35e+00
  ... (remaining 7159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 2586
       17.87 -    35.74: 340
       35.74 -    53.62: 92
       53.62 -    71.49: 14
       71.49 -    89.36: 14
  Dihedral angle restraints: 3046
    sinusoidal: 1208
      harmonic: 1838
  Sorted by residual:
  dihedral pdb=" CA  LEU B 120 "
           pdb=" C   LEU B 120 "
           pdb=" N   LEU B 121 "
           pdb=" CA  LEU B 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.02  -16.98     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  LEU A 120 "
           pdb=" C   LEU A 120 "
           pdb=" N   LEU A 121 "
           pdb=" CA  LEU A 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.03  -16.97     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CB  GLU A  60 "
           pdb=" CG  GLU A  60 "
           pdb=" CD  GLU A  60 "
           pdb=" OE1 GLU A  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.36   89.36     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 3043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 498
       0.025 -    0.050: 203
       0.050 -    0.075: 53
       0.075 -    0.100: 9
       0.100 -    0.125: 9
  Chirality restraints: 772
  Sorted by residual:
  chirality pdb=" CA  VAL A 112 "
            pdb=" N   VAL A 112 "
            pdb=" C   VAL A 112 "
            pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL B 112 "
            pdb=" N   VAL B 112 "
            pdb=" C   VAL B 112 "
            pdb=" CB  VAL B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  ILE B 189 "
            pdb=" N   ILE B 189 "
            pdb=" C   ILE B 189 "
            pdb=" CB  ILE B 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 769 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 312 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO B 313 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 313 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 313 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 312 "   -0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A 313 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 313 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 313 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  69 "   -0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO A  70 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1129
        2.77 -     3.30: 5182
        3.30 -     3.84: 8155
        3.84 -     4.37: 9401
        4.37 -     4.90: 15378
  Nonbonded interactions: 39245
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 137 "
            pdb=" OG1 THR A 141 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   LYS B 137 "
            pdb=" OG1 THR B 141 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   GLN A  44 "
            pdb=" OG1 THR A  48 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   GLN B  44 "
            pdb=" OG1 THR B  48 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   GLU A  38 "
            pdb=" OG1 THR A  41 "
     model   vdw
     2.310 3.040
  ... (remaining 39240 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.770
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
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   0.034   5296  Z= 0.197
  Angle     :  0.558   7.672   7164  Z= 0.320
  Chirality :  0.031   0.125    772
  Planarity :  0.003   0.035    888
  Dihedral  : 18.365  89.361   1858
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  7.46 %
    Allowed  : 17.16 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.29), residues: 614
  helix: -1.29 (0.18), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.07 (0.76), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 210 
 HIS   0.003   0.001   HIS A 196 
 PHE   0.007   0.001   PHE B 127 
 TYR   0.007   0.001   TYR A 172 
 ARG   0.005   0.000   ARG A 327 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 95
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 PHE cc_start: 0.7238 (t80) cc_final: 0.6972 (t80)
REVERT: A  127 PHE cc_start: 0.7398 (t80) cc_final: 0.7135 (t80)
REVERT: A  183 ILE cc_start: 0.7261 (mm) cc_final: 0.6926 (mt)
REVERT: A  228 MET cc_start: 0.7126 (mtm) cc_final: 0.6891 (ttm)
  outliers start: 40
  outliers final: 22
  residues processed: 130
  average time/residue: 0.1857
  time to fit residues: 30.9193
Evaluate side-chains
  90 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  304 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0040
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B 196 HIS
B 197 HIS
B 241 GLN
B 286 GLN
A 184 ASN
A 196 HIS
A 197 HIS
A 241 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.205043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.164790 restraints weight = 5678.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.168433 restraints weight = 3426.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.170632 restraints weight = 2539.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5296  Z= 0.186
  Angle     :  0.576   8.405   7164  Z= 0.295
  Chirality :  0.035   0.123    772
  Planarity :  0.005   0.057    888
  Dihedral  :  8.243  85.589    718
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 23.32 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.31), residues: 614
  helix:  1.27 (0.20), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.23 (0.62), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A  30 
 PHE   0.013   0.001   PHE B 195 
 TYR   0.013   0.001   TYR B 240 
 ARG   0.003   0.000   ARG B 327 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.900 
Fit side-chains
REVERT: B  118 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8204 (t)
REVERT: B  158 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6066 (tpt-90)
REVERT: B  291 LEU cc_start: 0.8976 (mm) cc_final: 0.8367 (tt)
REVERT: A   87 MET cc_start: 0.7523 (tpp) cc_final: 0.6881 (tpt)
REVERT: A  158 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6262 (tpt-90)
  outliers start: 20
  outliers final: 11
  residues processed: 98
  average time/residue: 0.2194
  time to fit residues: 27.8850
Evaluate side-chains
  81 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  304 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  30 HIS
A  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.202172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.161319 restraints weight = 5796.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.164773 restraints weight = 3555.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.166978 restraints weight = 2664.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5296  Z= 0.248
  Angle     :  0.564   6.131   7164  Z= 0.285
  Chirality :  0.036   0.120    772
  Planarity :  0.004   0.050    888
  Dihedral  :  7.431  85.064    704
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 26.12 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.32), residues: 614
  helix:  1.77 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.05 (0.60), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 210 
 HIS   0.001   0.001   HIS A 196 
 PHE   0.009   0.001   PHE A 235 
 TYR   0.016   0.002   TYR B 240 
 ARG   0.006   0.000   ARG B  34 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 PHE cc_start: 0.7514 (t80) cc_final: 0.6178 (m-10)
REVERT: B  158 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6225 (tpt-90)
REVERT: B  234 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6562 (mp10)
REVERT: A   88 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8195 (mtmt)
REVERT: A  127 PHE cc_start: 0.7348 (t80) cc_final: 0.6198 (m-10)
REVERT: A  158 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6325 (tpt-90)
REVERT: A  183 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7018 (mt)
  outliers start: 31
  outliers final: 19
  residues processed: 98
  average time/residue: 0.1717
  time to fit residues: 21.8222
Evaluate side-chains
  93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  304 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0040
   chunk 16 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 22 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
B 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.207730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.167583 restraints weight = 5845.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.170736 restraints weight = 3611.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.173192 restraints weight = 2739.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5296  Z= 0.158
  Angle     :  0.516   9.390   7164  Z= 0.254
  Chirality :  0.035   0.224    772
  Planarity :  0.003   0.036    888
  Dihedral  :  6.742  79.726    701
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 29.10 %
    Favored  : 65.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.33), residues: 614
  helix:  2.27 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.80 (0.62), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 210 
 HIS   0.001   0.000   HIS A 196 
 PHE   0.006   0.001   PHE A 235 
 TYR   0.014   0.001   TYR B 240 
 ARG   0.004   0.000   ARG A  34 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8115 (mtpt)
REVERT: B  158 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6052 (tpt-90)
REVERT: A   88 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8122 (mttt)
REVERT: A  127 PHE cc_start: 0.7348 (t80) cc_final: 0.6234 (m-10)
REVERT: A  158 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6119 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7448 (tp)
  outliers start: 28
  outliers final: 15
  residues processed: 96
  average time/residue: 0.1585
  time to fit residues: 20.1038
Evaluate side-chains
  82 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   91 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  304 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.204334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.163722 restraints weight = 5746.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.166870 restraints weight = 3505.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.169321 restraints weight = 2649.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5296  Z= 0.191
  Angle     :  0.538   7.676   7164  Z= 0.261
  Chirality :  0.036   0.211    772
  Planarity :  0.003   0.031    888
  Dihedral  :  5.438  51.125    694
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 28.92 %
    Favored  : 64.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.33), residues: 614
  helix:  2.46 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.87 (0.60), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 210 
 HIS   0.001   0.000   HIS B 196 
 PHE   0.009   0.001   PHE A 195 
 TYR   0.016   0.002   TYR B 240 
 ARG   0.004   0.000   ARG A  34 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 67
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 PHE cc_start: 0.7242 (t80) cc_final: 0.6110 (m-10)
REVERT: B  158 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6143 (tpt-90)
REVERT: B  208 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7341 (tp)
REVERT: B  234 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6408 (mp10)
REVERT: A   88 LYS cc_start: 0.8413 (mtmt) cc_final: 0.7994 (mtmt)
REVERT: A  127 PHE cc_start: 0.7401 (t80) cc_final: 0.6263 (m-10)
REVERT: A  158 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6228 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7357 (tp)
REVERT: A  228 MET cc_start: 0.7508 (mmm) cc_final: 0.7210 (mmm)
  outliers start: 34
  outliers final: 21
  residues processed: 93
  average time/residue: 0.2132
  time to fit residues: 26.4681
Evaluate side-chains
  92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   91 GLN
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  304 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4347 r_free = 0.4347 target = 0.203571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.162666 restraints weight = 5825.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.166216 restraints weight = 3561.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.168511 restraints weight = 2663.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5296  Z= 0.205
  Angle     :  0.552   8.976   7164  Z= 0.265
  Chirality :  0.035   0.218    772
  Planarity :  0.003   0.029    888
  Dihedral  :  5.259  47.075    694
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 29.85 %
    Favored  : 64.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.09 (0.33), residues: 614
  helix:  2.54 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.85 (0.61), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 210 
 HIS   0.001   0.000   HIS B 196 
 PHE   0.008   0.001   PHE A 195 
 TYR   0.021   0.002   TYR B 240 
 ARG   0.003   0.000   ARG A  34 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 70
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 PHE cc_start: 0.7264 (t80) cc_final: 0.6101 (m-10)
REVERT: B  158 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6183 (tpt-90)
REVERT: B  208 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7364 (tp)
REVERT: B  234 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6370 (mp10)
REVERT: B  309 MET cc_start: 0.7633 (tpp) cc_final: 0.7429 (tpp)
REVERT: A   88 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8061 (mttt)
REVERT: A  127 PHE cc_start: 0.7309 (t80) cc_final: 0.6146 (m-10)
REVERT: A  158 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6178 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7476 (tp)
REVERT: A  304 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5939 (mm-30)
REVERT: A  309 MET cc_start: 0.7634 (tpp) cc_final: 0.7396 (tpp)
  outliers start: 32
  outliers final: 22
  residues processed: 97
  average time/residue: 0.1462
  time to fit residues: 18.9193
Evaluate side-chains
  96 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   91 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4349 r_free = 0.4349 target = 0.203358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.162333 restraints weight = 5805.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.165873 restraints weight = 3565.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.168063 restraints weight = 2659.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5296  Z= 0.213
  Angle     :  0.556   8.864   7164  Z= 0.267
  Chirality :  0.036   0.229    772
  Planarity :  0.003   0.028    888
  Dihedral  :  5.139  43.019    694
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 30.04 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.33), residues: 614
  helix:  2.58 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.92 (0.60), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 210 
 HIS   0.001   0.000   HIS B 196 
 PHE   0.007   0.001   PHE A 235 
 TYR   0.016   0.002   TYR B 240 
 ARG   0.003   0.000   ARG A  34 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 PHE cc_start: 0.7271 (t80) cc_final: 0.6083 (m-10)
REVERT: B  158 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6207 (tpt-90)
REVERT: B  208 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7323 (tp)
REVERT: B  234 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6357 (mp10)
REVERT: A   88 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8046 (mttt)
REVERT: A  127 PHE cc_start: 0.7274 (t80) cc_final: 0.6091 (m-10)
REVERT: A  158 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6157 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7366 (tp)
REVERT: A  304 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6169 (mm-30)
  outliers start: 33
  outliers final: 21
  residues processed: 95
  average time/residue: 0.1710
  time to fit residues: 21.7170
Evaluate side-chains
  94 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 67
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4360 r_free = 0.4360 target = 0.204583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.163876 restraints weight = 5792.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.167126 restraints weight = 3543.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.169645 restraints weight = 2669.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5296  Z= 0.195
  Angle     :  0.568  10.825   7164  Z= 0.269
  Chirality :  0.035   0.236    772
  Planarity :  0.003   0.029    888
  Dihedral  :  4.936  38.432    694
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 31.90 %
    Favored  : 62.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.21 (0.33), residues: 614
  helix:  2.64 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.96 (0.60), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 210 
 HIS   0.001   0.000   HIS B 196 
 PHE   0.007   0.001   PHE A 195 
 TYR   0.024   0.002   TYR B 240 
 ARG   0.002   0.000   ARG A  34 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7862 (mtmt)
REVERT: B  158 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6237 (tpt-90)
REVERT: B  208 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7401 (tp)
REVERT: B  234 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6404 (mp10)
REVERT: B  240 TYR cc_start: 0.7384 (t80) cc_final: 0.6863 (t80)
REVERT: B  268 MET cc_start: 0.8436 (mmm) cc_final: 0.7774 (tpp)
REVERT: B  309 MET cc_start: 0.7661 (tpp) cc_final: 0.7370 (tpp)
REVERT: A   88 LYS cc_start: 0.8380 (mtmt) cc_final: 0.8041 (mttt)
REVERT: A  127 PHE cc_start: 0.7247 (t80) cc_final: 0.6123 (m-10)
REVERT: A  158 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6181 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7437 (tp)
REVERT: A  309 MET cc_start: 0.7634 (tpp) cc_final: 0.7318 (tpp)
  outliers start: 29
  outliers final: 18
  residues processed: 91
  average time/residue: 0.2345
  time to fit residues: 29.0174
Evaluate side-chains
  91 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4350 r_free = 0.4350 target = 0.203697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.161390 restraints weight = 5836.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.165299 restraints weight = 3403.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.167521 restraints weight = 2490.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5296  Z= 0.199
  Angle     :  0.580   9.354   7164  Z= 0.275
  Chirality :  0.035   0.245    772
  Planarity :  0.003   0.029    888
  Dihedral  :  3.941  18.007    686
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 32.28 %
    Favored  : 62.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.33), residues: 614
  helix:  2.68 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.85 (0.63), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 210 
 HIS   0.001   0.000   HIS B 196 
 PHE   0.007   0.001   PHE A 235 
 TYR   0.024   0.002   TYR B 240 
 ARG   0.010   0.000   ARG A  69 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7855 (mtmt)
REVERT: B  158 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6420 (tpt-90)
REVERT: B  208 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7603 (tp)
REVERT: B  234 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6541 (mp10)
REVERT: B  309 MET cc_start: 0.7670 (tpp) cc_final: 0.7456 (tpp)
REVERT: A   88 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8013 (mttt)
REVERT: A  127 PHE cc_start: 0.7248 (t80) cc_final: 0.6252 (m-10)
REVERT: A  158 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6314 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7663 (tp)
REVERT: A  240 TYR cc_start: 0.7348 (t80) cc_final: 0.6875 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 91
  average time/residue: 0.2295
  time to fit residues: 26.9525
Evaluate side-chains
  92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0030
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.4568

-------------------------------------------------------------------------------
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 = 0.4387 r_free = 0.4387 target = 0.207706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.167081 restraints weight = 5832.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.170706 restraints weight = 3558.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.172764 restraints weight = 2640.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5296  Z= 0.161
  Angle     :  0.562  10.500   7164  Z= 0.265
  Chirality :  0.034   0.248    772
  Planarity :  0.003   0.029    888
  Dihedral  :  3.878  17.910    686
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 32.28 %
    Favored  : 62.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.46 (0.33), residues: 614
  helix:  2.79 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.83 (0.64), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 210 
 HIS   0.001   0.000   HIS A 196 
 PHE   0.008   0.001   PHE B 127 
 TYR   0.014   0.001   TYR A 240 
 ARG   0.008   0.000   ARG A  69 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7857 (mtmt)
REVERT: B  158 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6175 (tpt-90)
REVERT: B  208 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7403 (tp)
REVERT: B  230 GLN cc_start: 0.7345 (tt0) cc_final: 0.6909 (tt0)
REVERT: B  234 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6361 (mp10)
REVERT: B  309 MET cc_start: 0.7688 (tpp) cc_final: 0.7420 (tpp)
REVERT: A   88 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8058 (mttt)
REVERT: A   89 GLU cc_start: 0.7661 (tt0) cc_final: 0.7434 (pt0)
REVERT: A  158 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6131 (tpt-90)
REVERT: A  208 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7412 (tp)
  outliers start: 29
  outliers final: 19
  residues processed: 91
  average time/residue: 0.1718
  time to fit residues: 20.6821
Evaluate side-chains
  91 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  158 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4373 r_free = 0.4373 target = 0.206175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.165310 restraints weight = 5861.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.168896 restraints weight = 3586.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.170874 restraints weight = 2668.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.4715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5296  Z= 0.182
  Angle     :  0.566   9.829   7164  Z= 0.267
  Chirality :  0.035   0.250    772
  Planarity :  0.003   0.030    888
  Dihedral  :  3.869  17.088    686
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 32.46 %
    Favored  : 62.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.46 (0.33), residues: 614
  helix:  2.80 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.88 (0.64), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 210 
 HIS   0.002   0.000   HIS B 196 
 PHE   0.010   0.001   PHE B 195 
 TYR   0.024   0.001   TYR A 240 
 ARG   0.008   0.000   ARG A  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2153.17 seconds
wall clock time: 40 minutes 18.94 seconds (2418.94 seconds total)