Starting phenix.real_space_refine
on Tue Feb 11 05:20:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hbn_34638/02_2025/8hbn_34638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hbn_34638/02_2025/8hbn_34638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hbn_34638/02_2025/8hbn_34638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hbn_34638/02_2025/8hbn_34638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hbn_34638/02_2025/8hbn_34638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hbn_34638/02_2025/8hbn_34638.cif"
  }
  resolution = 3.81
  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=   0.039
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      18      5.16       5
     C    2668      2.51       5
     N     722      2.21       5
     O     781      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4189
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2909
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 16, 'TRANS': 354}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 52
    Chain: "B"
      Number of atoms: 1280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1280
          Classifications: {'peptide': 165}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 9, 'TRANS': 155}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 3.84, per 1000 atoms: 0.92
  Number of scatterers: 4189
  At special positions: 0
  Unit cell: (70.808, 97.528, 85.504, 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      18     16.00
     O     781      8.00
     N     722      7.00
     C    2668      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: 1.03
  Conformation dependent library (CDL) restraints added in 557.0 milliseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1030

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      32.1% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.972A  pdb=" N   PHE A 106 " --> pdb=" O   ASP A 102 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 112 " --> pdb=" O   ARG A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 129
    Processing helix  chain 'A' and resid 130 through 135
      removed outlier: 3.586A  pdb=" N   ILE A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLN A 135 " --> pdb=" O   PRO A 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 130 through 135'
    Processing helix  chain 'A' and resid 148 through 159
      removed outlier: 3.806A  pdb=" N   MET A 152 " --> pdb=" O   MET A 148 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   MET A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 184
      removed outlier: 5.087A  pdb=" N   THR A 182 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ALA A 184 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 210
      removed outlier: 3.667A  pdb=" N   TRP A 209 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 230
      removed outlier: 5.903A  pdb=" N   LYS A 230 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 240
      removed outlier: 3.819A  pdb=" N   GLU A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   MET A 236 " --> pdb=" O   TYR A 232 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 260
      removed outlier: 3.657A  pdb=" N   VAL A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 295
      removed outlier: 3.537A  pdb=" N   ASN A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
      removed outlier: 3.715A  pdb=" N   LEU A 300 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN A 301 " --> pdb=" O   GLN A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 297 through 301'
    Processing helix  chain 'A' and resid 331 through 335
      removed outlier: 3.682A  pdb=" N   MET A 335 " --> pdb=" O   GLY A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 354
      removed outlier: 3.711A  pdb=" N   GLN A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 368
      removed outlier: 3.861A  pdb=" N   THR A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 31
      removed outlier: 3.797A  pdb=" N   ILE B  18 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B  27 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA B  28 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   HIS B  29 " --> pdb=" O   LYS B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 45
      removed outlier: 4.085A  pdb=" N   PHE B  41 " --> pdb=" O   LYS B  37 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLN B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU B  44 " --> pdb=" O   GLN B  40 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   PHE B  45 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 37 through 45'
    Processing helix  chain 'B' and resid 61 through 72
      removed outlier: 3.656A  pdb=" N   PHE B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN B  72 " --> pdb=" O   MET B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 160
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116
      removed outlier: 6.578A  pdb=" N   LEU A 122 " --> pdb=" O   ASN A 168 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 194 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU A 193 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271
      removed outlier: 6.704A  pdb=" N   PHE A 271 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
      removed outlier: 8.804A  pdb=" N   SER A 388 " --> pdb=" O   PHE A 271 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   SER A 444 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   VAL A 467 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ASP A 446 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   LEU A 465 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   THR A 448 " --> pdb=" O   ASP A 463 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   ASP A 463 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL A 450 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE A 459 " --> pdb=" O   VAL A 452 " (cutoff:3.500A)
      removed outlier: 9.710A  pdb=" N   ILE A 459 " --> pdb=" O   SER A 304 " (cutoff:3.500A)
      removed outlier: 9.911A  pdb=" N   GLN A 306 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ALA A 461 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU A 465 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A 355 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54
      removed outlier: 6.629A  pdb=" N   ARG B  51 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   TYR B 171 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ILE B  53 " --> pdb=" O   TYR B 171 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   MET B 173 " --> pdb=" O   ILE B  53 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   ILE B 166 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ASP B 154 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ASN B 172 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   THR B  93 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LYS B 101 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   LEU B  80 " --> pdb=" O   LYS B 101 " (cutoff:3.500A)

    120 hydrogen bonds defined for protein.
    312 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: 1.15

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 704
        1.31 -     1.44: 1113
        1.44 -     1.57: 2426
        1.57 -     1.70: 0
        1.70 -     1.83: 32
  Bond restraints: 4275
  Sorted by residual:
  bond pdb=" CA  SER A 441 "
       pdb=" CB  SER A 441 "
    ideal  model  delta    sigma   weight residual
    1.531  1.443  0.089 1.67e-02 3.59e+03 2.81e+01
  bond pdb=" N   CYS B  50 "
       pdb=" CA  CYS B  50 "
    ideal  model  delta    sigma   weight residual
    1.455  1.512 -0.057 1.25e-02 6.40e+03 2.08e+01
  bond pdb=" C   PRO A 379 "
       pdb=" O   PRO A 379 "
    ideal  model  delta    sigma   weight residual
    1.235  1.180  0.055 1.30e-02 5.92e+03 1.77e+01
  bond pdb=" CA  ALA B  79 "
       pdb=" CB  ALA B  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.461  0.069 1.69e-02 3.50e+03 1.68e+01
  bond pdb=" N   PRO A 379 "
       pdb=" CA  PRO A 379 "
    ideal  model  delta    sigma   weight residual
    1.469  1.417  0.052 1.28e-02 6.10e+03 1.62e+01
  ... (remaining 4270 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 5512
        2.72 -     5.44: 246
        5.44 -     8.16: 31
        8.16 -    10.88: 9
       10.88 -    13.60: 3
  Bond angle restraints: 5801
  Sorted by residual:
  angle pdb=" N   PRO A 379 "
        pdb=" CA  PRO A 379 "
        pdb=" CB  PRO A 379 "
      ideal   model   delta    sigma   weight residual
     103.25   93.14   10.11 1.05e+00 9.07e-01 9.27e+01
  angle pdb=" C   ARG A 217 "
        pdb=" CA  ARG A 217 "
        pdb=" CB  ARG A 217 "
      ideal   model   delta    sigma   weight residual
     110.35   96.75   13.60 1.78e+00 3.16e-01 5.83e+01
  angle pdb=" C   ILE B  52 "
        pdb=" N   ILE B  53 "
        pdb=" CA  ILE B  53 "
      ideal   model   delta    sigma   weight residual
     121.97  135.08  -13.11 1.80e+00 3.09e-01 5.30e+01
  angle pdb=" C   ASN A 437 "
        pdb=" CA  ASN A 437 "
        pdb=" CB  ASN A 437 "
      ideal   model   delta    sigma   weight residual
     110.42   98.43   11.99 1.99e+00 2.53e-01 3.63e+01
  angle pdb=" CA  PHE A 270 "
        pdb=" CB  PHE A 270 "
        pdb=" CG  PHE A 270 "
      ideal   model   delta    sigma   weight residual
     113.80  119.77   -5.97 1.00e+00 1.00e+00 3.56e+01
  ... (remaining 5796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 2154
       16.50 -    33.00: 287
       33.00 -    49.49: 113
       49.49 -    65.99: 27
       65.99 -    82.49: 8
  Dihedral angle restraints: 2589
    sinusoidal: 1012
      harmonic: 1577
  Sorted by residual:
  dihedral pdb=" C   ARG A 217 "
           pdb=" N   ARG A 217 "
           pdb=" CA  ARG A 217 "
           pdb=" CB  ARG A 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -103.86  -18.74     0      2.50e+00 1.60e-01 5.62e+01
  dihedral pdb=" N   PRO A 379 "
           pdb=" C   PRO A 379 "
           pdb=" CA  PRO A 379 "
           pdb=" CB  PRO A 379 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10   98.73   16.37     0      2.50e+00 1.60e-01 4.29e+01
  dihedral pdb=" C   PRO A 379 "
           pdb=" N   PRO A 379 "
           pdb=" CA  PRO A 379 "
           pdb=" CB  PRO A 379 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -104.40  -16.30     0      2.50e+00 1.60e-01 4.25e+01
  ... (remaining 2586 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 573
       0.081 -    0.162: 70
       0.162 -    0.243: 17
       0.243 -    0.325: 4
       0.325 -    0.406: 1
  Chirality restraints: 665
  Sorted by residual:
  chirality pdb=" CA  ARG A 217 "
            pdb=" N   ARG A 217 "
            pdb=" C   ARG A 217 "
            pdb=" CB  ARG A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.11e+00
  chirality pdb=" CA  ASP B  34 "
            pdb=" N   ASP B  34 "
            pdb=" C   ASP B  34 "
            pdb=" CB  ASP B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  ASN A 189 "
            pdb=" N   ASN A 189 "
            pdb=" C   ASN A 189 "
            pdb=" CB  ASN A 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 662 not shown)

  Planarity restraints: 748
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  79 "   -0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   ALA B  79 "    0.066 2.00e-02 2.50e+03
        pdb=" O   ALA B  79 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU B  80 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 252 "    0.020 2.00e-02 2.50e+03   3.81e-02 1.45e+01
        pdb=" C   ARG A 252 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ARG A 252 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ASP A 253 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 265 "    0.017 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   MET A 265 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   MET A 265 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LYS A 266 "    0.021 2.00e-02 2.50e+03
  ... (remaining 745 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1073
        2.78 -     3.31: 3966
        3.31 -     3.84: 6284
        3.84 -     4.37: 7294
        4.37 -     4.90: 12513
  Nonbonded interactions: 31130
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 278 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ASP A 102 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" CB  ASN A 437 "
            pdb=" N   ASN A 438 "
     model   vdw
     2.325 2.816
  nonbonded pdb=" O   GLN A 255 "
            pdb=" C   LYS A 256 "
     model   vdw
     2.328 3.270
  nonbonded pdb=" O   LEU A 257 "
            pdb=" N   THR A 259 "
     model   vdw
     2.331 3.120
  ... (remaining 31125 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.220
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
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      :  0.007   0.089   4275  Z= 0.455
  Angle     :  1.240  13.597   5801  Z= 0.781
  Chirality :  0.063   0.406    665
  Planarity :  0.007   0.090    748
  Dihedral  : 18.565  82.489   1559
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  2.65 %
    Allowed  :  7.39 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 28.10 %
    Favored  : 65.80 %
  Cbeta Deviations :  0.97 %
  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: -1.66 (0.36), residues: 528
  helix: -1.59 (0.46), residues: 118
  sheet: -0.36 (0.59), residues: 98
  loop : -1.12 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 209 
 HIS   0.004   0.001   HIS B  86 
 PHE   0.023   0.002   PHE A 270 
 TYR   0.021   0.002   TYR A 382 
 ARG   0.006   0.001   ARG B 109 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8332 (mmt)
REVERT: A  379 PRO cc_start: 0.9471 (OUTLIER) cc_final: 0.8857 (Cg_exo)
REVERT: B   32 ASP cc_start: 0.8854 (t0) cc_final: 0.8620 (t0)
REVERT: B  134 MET cc_start: 0.7455 (ptt) cc_final: 0.6901 (tpt)
REVERT: B  167 SER cc_start: 0.8630 (p) cc_final: 0.8350 (p)
  outliers start: 28
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1690
  time to fit residues: 25.5961
Evaluate side-chains
  80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  379 PRO
Chi-restraints excluded: chain A residue  426 ARG
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue   34 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 40 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
A 380 ASN
B  49 ASN
B  61 GLN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 HIS
B  97 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.075381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.059368 restraints weight = 17692.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.061072 restraints weight = 10324.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.062234 restraints weight = 7170.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4275  Z= 0.224
  Angle     :  0.747   7.272   5801  Z= 0.386
  Chirality :  0.049   0.186    665
  Planarity :  0.005   0.063    748
  Dihedral  :  8.710  81.570    596
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  5.68 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 26.58 %
    Favored  : 66.01 %
  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: -1.03 (0.37), residues: 528
  helix: -0.84 (0.45), residues: 137
  sheet: -0.38 (0.51), residues: 111
  loop : -0.62 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 292 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.011   0.001   PHE B 104 
 TYR   0.014   0.002   TYR B  85 
 ARG   0.005   0.001   ARG A 114 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8804 (tt)
REVERT: A  302 LEU cc_start: 0.9378 (mt) cc_final: 0.9167 (mp)
REVERT: A  335 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8817 (mmt)
REVERT: A  343 LYS cc_start: 0.9312 (tppt) cc_final: 0.9093 (tptt)
REVERT: A  398 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8863 (p)
REVERT: A  454 MET cc_start: 0.7553 (tpt) cc_final: 0.7213 (tpt)
REVERT: B   32 ASP cc_start: 0.8967 (t0) cc_final: 0.8565 (t0)
REVERT: B   38 LEU cc_start: 0.9197 (mt) cc_final: 0.8982 (pp)
REVERT: B  134 MET cc_start: 0.7393 (ptt) cc_final: 0.6879 (tpt)
REVERT: B  183 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8461 (mmmt)
  outliers start: 34
  outliers final: 16
  residues processed: 99
  average time/residue: 0.1336
  time to fit residues: 17.3960
Evaluate side-chains
  85 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  433 ASN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  136 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0040
   chunk 29 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 ASN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.071541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.055938 restraints weight = 17782.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.057530 restraints weight = 10407.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.058603 restraints weight = 7295.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4275  Z= 0.233
  Angle     :  0.668   8.691   5801  Z= 0.342
  Chirality :  0.046   0.172    665
  Planarity :  0.004   0.053    748
  Dihedral  :  6.984  81.888    576
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.25 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 24.62 %
    Favored  : 68.41 %
  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: -0.61 (0.37), residues: 528
  helix: -0.41 (0.45), residues: 137
  sheet:  0.04 (0.52), residues: 105
  loop : -0.48 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 292 
 HIS   0.002   0.001   HIS A 373 
 PHE   0.012   0.001   PHE B  65 
 TYR   0.012   0.001   TYR A 382 
 ARG   0.002   0.000   ARG B 109 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8951 (tt)
REVERT: A  335 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8897 (mmm)
REVERT: A  374 HIS cc_start: 0.8218 (m-70) cc_final: 0.7998 (m-70)
REVERT: A  384 MET cc_start: 0.8393 (tmm) cc_final: 0.8089 (tmm)
REVERT: A  398 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8925 (p)
REVERT: A  429 ASN cc_start: 0.9167 (p0) cc_final: 0.8947 (p0)
REVERT: A  454 MET cc_start: 0.7489 (tpt) cc_final: 0.7227 (tpt)
REVERT: B   32 ASP cc_start: 0.8982 (t0) cc_final: 0.8588 (t0)
REVERT: B  106 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8649 (mp0)
REVERT: B  134 MET cc_start: 0.7402 (ptt) cc_final: 0.6878 (tpt)
REVERT: B  182 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9337 (mm)
REVERT: B  183 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8875 (mmmt)
  outliers start: 32
  outliers final: 20
  residues processed: 84
  average time/residue: 0.1278
  time to fit residues: 14.4573
Evaluate side-chains
  78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  182 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 ASN
A 290 ASN
A 380 ASN
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.068741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.053213 restraints weight = 18443.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.054723 restraints weight = 10836.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.055765 restraints weight = 7678.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4275  Z= 0.270
  Angle     :  0.662   8.947   5801  Z= 0.339
  Chirality :  0.046   0.145    665
  Planarity :  0.004   0.049    748
  Dihedral  :  7.035  80.880    576
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.01 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 25.27 %
    Favored  : 67.76 %
  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: -0.71 (0.37), residues: 528
  helix: -0.18 (0.45), residues: 138
  sheet: -0.20 (0.52), residues: 96
  loop : -0.63 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.016   0.002   PHE A 284 
 TYR   0.016   0.002   TYR B  85 
 ARG   0.002   0.001   ARG A 468 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 50
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9064 (tt)
REVERT: A  335 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8902 (mmm)
REVERT: A  384 MET cc_start: 0.8473 (tmm) cc_final: 0.8122 (tmm)
REVERT: A  398 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8945 (p)
REVERT: A  454 MET cc_start: 0.7516 (tpt) cc_final: 0.6896 (tpt)
REVERT: B   32 ASP cc_start: 0.8999 (t0) cc_final: 0.8620 (t0)
REVERT: B   68 MET cc_start: 0.9178 (ptm) cc_final: 0.8692 (ppp)
REVERT: B  134 MET cc_start: 0.7255 (ptt) cc_final: 0.6551 (tpt)
REVERT: B  167 SER cc_start: 0.9227 (t) cc_final: 0.9001 (p)
REVERT: B  182 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9218 (mm)
REVERT: B  183 LYS cc_start: 0.9259 (mmmt) cc_final: 0.8938 (mmmt)
  outliers start: 32
  outliers final: 23
  residues processed: 76
  average time/residue: 0.1300
  time to fit residues: 13.3088
Evaluate side-chains
  73 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 46
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  182 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 22 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.069862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.054156 restraints weight = 18626.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.055760 restraints weight = 10903.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.056851 restraints weight = 7660.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4275  Z= 0.178
  Angle     :  0.646   9.748   5801  Z= 0.319
  Chirality :  0.045   0.147    665
  Planarity :  0.004   0.045    748
  Dihedral  :  6.938  83.944    576
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.82 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 25.27 %
    Favored  : 67.76 %
  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: -0.66 (0.37), residues: 528
  helix: -0.07 (0.46), residues: 132
  sheet: -0.37 (0.52), residues: 99
  loop : -0.55 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 292 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.012   0.001   PHE A 284 
 TYR   0.014   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B  51 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 56
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9050 (tt)
REVERT: A  335 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8975 (mmm)
REVERT: A  384 MET cc_start: 0.8533 (tmm) cc_final: 0.7947 (tmm)
REVERT: A  398 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8946 (p)
REVERT: A  454 MET cc_start: 0.7396 (tpt) cc_final: 0.6826 (tpt)
REVERT: B   32 ASP cc_start: 0.8964 (t0) cc_final: 0.8598 (t0)
REVERT: B   68 MET cc_start: 0.9095 (ptm) cc_final: 0.8657 (ppp)
REVERT: B  134 MET cc_start: 0.7209 (ptt) cc_final: 0.6536 (tpt)
REVERT: B  167 SER cc_start: 0.9189 (t) cc_final: 0.8962 (p)
REVERT: B  183 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8956 (mmmt)
  outliers start: 32
  outliers final: 23
  residues processed: 79
  average time/residue: 0.1231
  time to fit residues: 13.0917
Evaluate side-chains
  75 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 49
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0670
   chunk 27 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0980
   chunk 21 optimal weight:    0.0670
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
B  86 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.070587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.054728 restraints weight = 18307.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.056287 restraints weight = 10866.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.057373 restraints weight = 7708.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.4435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4275  Z= 0.174
  Angle     :  0.672  11.932   5801  Z= 0.322
  Chirality :  0.045   0.142    665
  Planarity :  0.004   0.042    748
  Dihedral  :  6.804  82.635    576
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.44 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 27.23 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.62 (0.36), residues: 528
  helix: -0.25 (0.46), residues: 126
  sheet: -0.31 (0.53), residues: 99
  loop : -0.43 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 292 
 HIS   0.003   0.001   HIS B  86 
 PHE   0.015   0.001   PHE A 284 
 TYR   0.022   0.001   TYR B  85 
 ARG   0.003   0.000   ARG A 339 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  335 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9003 (mmm)
REVERT: A  384 MET cc_start: 0.8536 (tmm) cc_final: 0.8086 (tmm)
REVERT: A  398 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8996 (p)
REVERT: A  454 MET cc_start: 0.7807 (tpt) cc_final: 0.7413 (tpt)
REVERT: B   32 ASP cc_start: 0.8910 (t0) cc_final: 0.8565 (t0)
REVERT: B   68 MET cc_start: 0.9097 (ptm) cc_final: 0.8633 (ppp)
REVERT: B  106 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8493 (mp0)
REVERT: B  134 MET cc_start: 0.7214 (ptt) cc_final: 0.6555 (tpt)
REVERT: B  167 SER cc_start: 0.9120 (t) cc_final: 0.8881 (p)
REVERT: B  182 LEU cc_start: 0.9509 (mm) cc_final: 0.9199 (mm)
REVERT: B  183 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8936 (mmmt)
  outliers start: 24
  outliers final: 19
  residues processed: 76
  average time/residue: 0.1272
  time to fit residues: 13.0108
Evaluate side-chains
  80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0870
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.068955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.053619 restraints weight = 18688.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.055191 restraints weight = 11043.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.056246 restraints weight = 7784.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4275  Z= 0.210
  Angle     :  0.663  11.411   5801  Z= 0.320
  Chirality :  0.045   0.142    665
  Planarity :  0.003   0.040    748
  Dihedral  :  6.867  82.962    576
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.63 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 28.10 %
    Favored  : 66.45 %
  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: -0.64 (0.37), residues: 528
  helix: -0.16 (0.46), residues: 132
  sheet: -0.46 (0.51), residues: 99
  loop : -0.44 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 292 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.010   0.001   PHE A 403 
 TYR   0.013   0.001   TYR A 428 
 ARG   0.002   0.000   ARG A 468 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 55
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  326 ASP cc_start: 0.8824 (t0) cc_final: 0.8545 (t0)
REVERT: A  335 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8963 (mmm)
REVERT: A  384 MET cc_start: 0.8570 (tmm) cc_final: 0.8110 (tmm)
REVERT: A  398 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8970 (p)
REVERT: A  465 LEU cc_start: 0.9527 (tp) cc_final: 0.9276 (tp)
REVERT: B   32 ASP cc_start: 0.8945 (t0) cc_final: 0.8621 (t0)
REVERT: B   68 MET cc_start: 0.9094 (ptm) cc_final: 0.8685 (ppp)
REVERT: B  106 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8337 (mp0)
REVERT: B  134 MET cc_start: 0.7240 (ptt) cc_final: 0.6556 (tpt)
REVERT: B  167 SER cc_start: 0.9098 (t) cc_final: 0.8864 (p)
REVERT: B  183 LYS cc_start: 0.9323 (mmmt) cc_final: 0.8973 (mmmt)
  outliers start: 25
  outliers final: 22
  residues processed: 72
  average time/residue: 0.1413
  time to fit residues: 13.8375
Evaluate side-chains
  78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  173 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0770
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6940

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.069177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.053846 restraints weight = 18444.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.055370 restraints weight = 10888.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.056429 restraints weight = 7699.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4275  Z= 0.191
  Angle     :  0.678  11.197   5801  Z= 0.324
  Chirality :  0.044   0.142    665
  Planarity :  0.003   0.039    748
  Dihedral  :  6.831  82.910    576
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.63 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 28.32 %
    Favored  : 66.23 %
  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: -0.58 (0.37), residues: 528
  helix: -0.13 (0.46), residues: 132
  sheet: -0.33 (0.51), residues: 97
  loop : -0.44 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 292 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.008   0.001   PHE A 284 
 TYR   0.012   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 109 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 ASP cc_start: 0.8829 (t0) cc_final: 0.8527 (t0)
REVERT: A  335 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.9009 (mmm)
REVERT: A  384 MET cc_start: 0.8603 (tmm) cc_final: 0.8126 (tmm)
REVERT: A  398 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9012 (p)
REVERT: A  465 LEU cc_start: 0.9534 (tp) cc_final: 0.9301 (tp)
REVERT: B   32 ASP cc_start: 0.8965 (t0) cc_final: 0.8286 (p0)
REVERT: B   68 MET cc_start: 0.9047 (ptm) cc_final: 0.8746 (ppp)
REVERT: B  106 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8443 (mp0)
REVERT: B  134 MET cc_start: 0.7248 (ptt) cc_final: 0.6557 (tpt)
REVERT: B  167 SER cc_start: 0.9047 (t) cc_final: 0.8842 (p)
REVERT: B  182 LEU cc_start: 0.9504 (mm) cc_final: 0.9066 (mm)
REVERT: B  183 LYS cc_start: 0.9318 (mmmt) cc_final: 0.8957 (mmmt)
  outliers start: 25
  outliers final: 22
  residues processed: 77
  average time/residue: 0.1236
  time to fit residues: 12.9028
Evaluate side-chains
  81 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  173 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    0.3980
   chunk 3 optimal weight:    0.0570
   chunk 23 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.3298

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.070520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.054912 restraints weight = 18537.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.056513 restraints weight = 10868.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.057634 restraints weight = 7648.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   4275  Z= 0.167
  Angle     :  0.676  11.619   5801  Z= 0.322
  Chirality :  0.044   0.141    665
  Planarity :  0.003   0.038    748
  Dihedral  :  6.714  82.231    576
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.63 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 29.63 %
    Favored  : 65.58 %
  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: -0.51 (0.37), residues: 528
  helix: -0.17 (0.47), residues: 126
  sheet: -0.21 (0.51), residues: 97
  loop : -0.36 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 292 
 HIS   0.002   0.000   HIS A 373 
 PHE   0.006   0.001   PHE A 403 
 TYR   0.012   0.001   TYR A 428 
 ARG   0.002   0.000   ARG A 447 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 ASP cc_start: 0.8827 (t0) cc_final: 0.8518 (t0)
REVERT: A  335 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.9078 (mmm)
REVERT: A  384 MET cc_start: 0.8771 (tmm) cc_final: 0.8297 (tmm)
REVERT: B   32 ASP cc_start: 0.8942 (t0) cc_final: 0.8206 (p0)
REVERT: B   68 MET cc_start: 0.9047 (ptm) cc_final: 0.8659 (ppp)
REVERT: B  106 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8380 (mp0)
REVERT: B  134 MET cc_start: 0.7238 (ptt) cc_final: 0.6556 (tpt)
REVERT: B  182 LEU cc_start: 0.9493 (mm) cc_final: 0.9046 (mm)
REVERT: B  183 LYS cc_start: 0.9315 (mmmt) cc_final: 0.8941 (mmmt)
  outliers start: 22
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1192
  time to fit residues: 12.2605
Evaluate side-chains
  77 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  173 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 30 optimal weight:    0.0060
   chunk 43 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.069428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.054030 restraints weight = 18741.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.055621 restraints weight = 11004.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056703 restraints weight = 7748.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4275  Z= 0.181
  Angle     :  0.692  11.667   5801  Z= 0.325
  Chirality :  0.044   0.144    665
  Planarity :  0.003   0.038    748
  Dihedral  :  6.695  81.973    576
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.06 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 30.28 %
    Favored  : 65.80 %
  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: -0.52 (0.37), residues: 528
  helix: -0.13 (0.46), residues: 132
  sheet: -0.26 (0.51), residues: 96
  loop : -0.39 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 449 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.008   0.001   PHE A 403 
 TYR   0.011   0.001   TYR A 428 
 ARG   0.003   0.000   ARG A 447 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 ASP cc_start: 0.8914 (t0) cc_final: 0.8613 (t0)
REVERT: A  335 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9093 (mmm)
REVERT: A  384 MET cc_start: 0.8646 (tmm) cc_final: 0.8224 (tmm)
REVERT: B   32 ASP cc_start: 0.8943 (t0) cc_final: 0.8236 (p0)
REVERT: B   68 MET cc_start: 0.9055 (ptm) cc_final: 0.8673 (ppp)
REVERT: B  106 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8483 (mp0)
REVERT: B  134 MET cc_start: 0.7267 (ptt) cc_final: 0.6564 (tpt)
REVERT: B  182 LEU cc_start: 0.9493 (mm) cc_final: 0.9047 (mm)
REVERT: B  183 LYS cc_start: 0.9339 (mmmt) cc_final: 0.8975 (mmmt)
  outliers start: 18
  outliers final: 16
  residues processed: 69
  average time/residue: 0.1285
  time to fit residues: 11.9936
Evaluate side-chains
  75 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  173 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 3 optimal weight:    0.0170
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0770
   chunk 9 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5776

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.069506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.054270 restraints weight = 18551.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.055835 restraints weight = 10951.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.056928 restraints weight = 7717.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4275  Z= 0.178
  Angle     :  0.688  11.765   5801  Z= 0.323
  Chirality :  0.044   0.143    665
  Planarity :  0.003   0.038    748
  Dihedral  :  6.688  82.072    576
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.25 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 30.50 %
    Favored  : 65.36 %
  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: -0.44 (0.37), residues: 528
  helix: -0.01 (0.46), residues: 133
  sheet: -0.44 (0.51), residues: 99
  loop : -0.26 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 449 
 HIS   0.002   0.001   HIS A 373 
 PHE   0.008   0.001   PHE A 403 
 TYR   0.010   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 109 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1754.31 seconds
wall clock time: 32 minutes 4.87 seconds (1924.87 seconds total)