Starting phenix.real_space_refine
on Thu Mar  5 02:40:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ul6_26593/03_2026/7ul6_26593.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ul6_26593/03_2026/7ul6_26593.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ul6_26593/03_2026/7ul6_26593.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ul6_26593/03_2026/7ul6_26593.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ul6_26593/03_2026/7ul6_26593.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ul6_26593/03_2026/7ul6_26593.map"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.103
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6628 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4272      2.51       5
     N    1146      2.21       5
     O    1212      1.98       5
     H    6614      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13268
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 6634
          Classifications: {'peptide': 439}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 417}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 6634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 6634
          Classifications: {'peptide': 439}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 417}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 30
  Time building chain proxies: 2.41, per 1000 atoms: 0.18
  Number of scatterers: 13268
  At special positions: 0
  Unit cell: (89.925, 91.575, 103.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     O    1212      8.00
     N    1146      7.00
     C    4272      6.00
     H    6614      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 337 " - pdb=" SG  CYS A 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 337 " - pdb=" SG  CYS B 363 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 398.9 milliseconds
  

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1628

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      52.1% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 55
    Processing helix  chain 'A' and resid 96 through 111
      removed outlier: 4.000A  pdb=" N   PHE A 100 " --> pdb=" O   MET A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 139 through 145
      removed outlier: 3.680A  pdb=" N   PHE A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 160
      removed outlier: 3.693A  pdb=" N   ARG A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 171
    Processing helix  chain 'A' and resid 189 through 203
      removed outlier: 3.913A  pdb=" N   VAL A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 214
    Processing helix  chain 'A' and resid 254 through 261
      Proline residue:  A 259  - end of helix
    Processing helix  chain 'A' and resid 267 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.384A  pdb=" N   ALA A 282 " --> pdb=" O   HIS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 295
      removed outlier: 3.628A  pdb=" N   TRP A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 344
      No H-bonds generated for 'chain 'A' and resid 342 through 344'
    Processing helix  chain 'A' and resid 361 through 373
      removed outlier: 3.580A  pdb=" N   ILE A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASP A 367 " --> pdb=" O   CYS A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 414
    Processing helix  chain 'A' and resid 434 through 455
      removed outlier: 4.532A  pdb=" N   VAL A 439 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
      removed outlier: 3.906A  pdb=" N   ALA A 445 " --> pdb=" O   GLY A 441 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 459 through 467
    Processing helix  chain 'A' and resid 468 through 471
    Processing helix  chain 'A' and resid 472 through 495
    Processing helix  chain 'B' and resid 40 through 55
    Processing helix  chain 'B' and resid 96 through 111
      removed outlier: 3.820A  pdb=" N   PHE B 100 " --> pdb=" O   MET B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 123
    Processing helix  chain 'B' and resid 139 through 145
      removed outlier: 3.577A  pdb=" N   PHE B 143 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 159
      removed outlier: 3.663A  pdb=" N   ARG B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 172
    Processing helix  chain 'B' and resid 189 through 203
      removed outlier: 3.896A  pdb=" N   VAL B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
    Processing helix  chain 'B' and resid 254 through 258
      removed outlier: 3.581A  pdb=" N   VAL B 258 " --> pdb=" O   ARG B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 279
    Processing helix  chain 'B' and resid 284 through 295
      removed outlier: 3.613A  pdb=" N   TRP B 295 " --> pdb=" O   MET B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 344
      No H-bonds generated for 'chain 'B' and resid 342 through 344'
    Processing helix  chain 'B' and resid 356 through 360
    Processing helix  chain 'B' and resid 361 through 372
    Processing helix  chain 'B' and resid 381 through 416
    Processing helix  chain 'B' and resid 434 through 455
      removed outlier: 4.596A  pdb=" N   VAL B 439 " --> pdb=" O   ILE B 435 " (cutoff:3.500A)
      Proline residue:  B 440  - end of helix
      removed outlier: 4.054A  pdb=" N   ALA B 445 " --> pdb=" O   GLY B 441 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
    Processing helix  chain 'B' and resid 459 through 467
    Processing helix  chain 'B' and resid 468 through 471
    Processing helix  chain 'B' and resid 472 through 495
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.468A  pdb=" N   LYS A  83 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER A 335 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.468A  pdb=" N   LYS A  83 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER A 335 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92
    Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135
    Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242
    Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 84
      removed outlier: 6.426A  pdb=" N   LYS B  83 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER B 335 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84
      removed outlier: 6.426A  pdb=" N   LYS B  83 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER B 335 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92
    Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 135
    Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 242

    412 hydrogen bonds defined for protein.
    1134 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: 3.41

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6612
        1.03 -     1.23: 4
        1.23 -     1.42: 2816
        1.42 -     1.62: 3936
        1.62 -     1.81: 42
  Bond restraints: 13410
  Sorted by residual:
  bond pdb=" CB  PRO B 151 "
       pdb=" CG  PRO B 151 "
    ideal  model  delta    sigma   weight residual
    1.492  1.604 -0.112 5.00e-02 4.00e+02 4.99e+00
  bond pdb=" CG  PRO A 151 "
       pdb=" CD  PRO A 151 "
    ideal  model  delta    sigma   weight residual
    1.503  1.579 -0.076 3.40e-02 8.65e+02 4.94e+00
  bond pdb=" CB  PRO A 151 "
       pdb=" CG  PRO A 151 "
    ideal  model  delta    sigma   weight residual
    1.492  1.598 -0.106 5.00e-02 4.00e+02 4.47e+00
  bond pdb=" N   PRO A 151 "
       pdb=" CA  PRO A 151 "
    ideal  model  delta    sigma   weight residual
    1.469  1.454  0.015 1.28e-02 6.10e+03 1.33e+00
  bond pdb=" CG  PRO B 151 "
       pdb=" CD  PRO B 151 "
    ideal  model  delta    sigma   weight residual
    1.503  1.538 -0.035 3.40e-02 8.65e+02 1.04e+00
  ... (remaining 13405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 23626
        1.48 -     2.95: 562
        2.95 -     4.43: 53
        4.43 -     5.91: 6
        5.91 -     7.38: 3
  Bond angle restraints: 24250
  Sorted by residual:
  angle pdb=" CA  PRO B 151 "
        pdb=" N   PRO B 151 "
        pdb=" CD  PRO B 151 "
      ideal   model   delta    sigma   weight residual
     112.00  104.62    7.38 1.40e+00 5.10e-01 2.78e+01
  angle pdb=" CA  PRO A 151 "
        pdb=" N   PRO A 151 "
        pdb=" CD  PRO A 151 "
      ideal   model   delta    sigma   weight residual
     112.00  104.76    7.24 1.40e+00 5.10e-01 2.68e+01
  angle pdb=" N   ALA A 364 "
        pdb=" CA  ALA A 364 "
        pdb=" C   ALA A 364 "
      ideal   model   delta    sigma   weight residual
     113.43  107.77    5.66 1.26e+00 6.30e-01 2.02e+01
  angle pdb=" N   ILE B 359 "
        pdb=" CA  ILE B 359 "
        pdb=" C   ILE B 359 "
      ideal   model   delta    sigma   weight residual
     111.91  108.67    3.24 8.90e-01 1.26e+00 1.33e+01
  angle pdb=" N   ILE A 359 "
        pdb=" CA  ILE A 359 "
        pdb=" C   ILE A 359 "
      ideal   model   delta    sigma   weight residual
     112.80  108.74    4.06 1.15e+00 7.56e-01 1.24e+01
  ... (remaining 24245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5780
       17.96 -    35.91: 374
       35.91 -    53.87: 141
       53.87 -    71.83: 30
       71.83 -    89.78: 9
  Dihedral angle restraints: 6334
    sinusoidal: 3392
      harmonic: 2942
  Sorted by residual:
  dihedral pdb=" CB  CYS B 337 "
           pdb=" SG  CYS B 337 "
           pdb=" SG  CYS B 363 "
           pdb=" CB  CYS B 363 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.88   58.88     1      1.00e+01 1.00e-02 4.64e+01
  dihedral pdb=" CB  CYS A 337 "
           pdb=" SG  CYS A 337 "
           pdb=" SG  CYS A 363 "
           pdb=" CB  CYS A 363 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.45   57.45     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" CA  TRP B 315 "
           pdb=" C   TRP B 315 "
           pdb=" N   PHE B 316 "
           pdb=" CA  PHE B 316 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 6331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 646
       0.029 -    0.057: 275
       0.057 -    0.086: 94
       0.086 -    0.114: 49
       0.114 -    0.143: 16
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  VAL B  73 "
            pdb=" N   VAL B  73 "
            pdb=" C   VAL B  73 "
            pdb=" CB  VAL B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  VAL A  73 "
            pdb=" N   VAL A  73 "
            pdb=" C   VAL A  73 "
            pdb=" CB  VAL A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  VAL A 301 "
            pdb=" N   VAL A 301 "
            pdb=" C   VAL A 301 "
            pdb=" CB  VAL A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 2020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 150 "   -0.058 5.00e-02 4.00e+02   8.45e-02 1.14e+01
        pdb=" N   PRO B 151 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO B 151 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 151 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 474 "   -0.049 5.00e-02 4.00e+02   7.33e-02 8.60e+00
        pdb=" N   PRO A 475 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 475 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 475 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 150 "    0.051 5.00e-02 4.00e+02   7.29e-02 8.51e+00
        pdb=" N   PRO A 151 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO A 151 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 151 "    0.040 5.00e-02 4.00e+02
  ... (remaining 2017 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.20: 797
        2.20 -     2.80: 27454
        2.80 -     3.40: 37046
        3.40 -     4.00: 48147
        4.00 -     4.60: 74312
  Nonbonded interactions: 187756
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 314 "
            pdb=" HD1 HIS A 327 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" OD1 ASN B  85 "
            pdb=" HH  TYR B  91 "
     model   vdw
     1.641 2.450
  nonbonded pdb="HD21 ASN B 130 "
            pdb=" OD1 ASN B 173 "
     model   vdw
     1.654 2.450
  nonbonded pdb=" HG1 THR A 101 "
            pdb=" O   PRO A 259 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" OD1 ASN A  85 "
            pdb=" HH  TYR A  91 "
     model   vdw
     1.668 2.450
  ... (remaining 187751 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     14.130
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.112   6798  Z= 0.124
  Angle     :  0.603   7.381   9270  Z= 0.354
  Chirality :  0.041   0.143   1080
  Planarity :  0.006   0.084   1190
  Dihedral  : 14.366  89.782   2398
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 12.28 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.29), residues: 866
  helix:  1.55 (0.27), residues: 382
  sheet: -1.14 (0.60), residues: 62
  loop :  0.76 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 255 
 TYR   0.012   0.001   TYR B 131 
 PHE   0.007   0.001   PHE A 483 
 TRP   0.029   0.002   TRP B 273 
 HIS   0.007   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6796)
  covalent geometry    : angle       0.60268 ( 9266)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.81001 (    4)
  hydrogen bonds       : bond        0.16017 (  368)
  hydrogen bonds       : angle       7.13124 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  135 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 LYS cc_start: 0.6960 (mptt) cc_final: 0.6650 (mptt)
REVERT: A  367 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8357 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1475
  time to fit residues: 27.6551
Evaluate side-chains
  119 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 130 ASN
B 130 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.183905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.151709 restraints weight = 22879.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.158774 restraints weight = 11846.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.163661 restraints weight = 7571.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.166890 restraints weight = 5397.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.169130 restraints weight = 4159.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6798  Z= 0.132
  Angle     :  0.564   5.619   9270  Z= 0.300
  Chirality :  0.042   0.154   1080
  Planarity :  0.005   0.051   1190
  Dihedral  :  5.003  55.618    944
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.13 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.29), residues: 866
  helix:  1.46 (0.26), residues: 412
  sheet: -0.46 (0.62), residues: 68
  loop :  0.37 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.009   0.001   TYR B 369 
 PHE   0.010   0.001   PHE A 100 
 TRP   0.019   0.002   TRP B 273 
 HIS   0.007   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6796)
  covalent geometry    : angle       0.56330 ( 9266)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       1.04346 (    4)
  hydrogen bonds       : bond        0.03916 (  368)
  hydrogen bonds       : angle       5.05587 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  150 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 LYS cc_start: 0.6925 (mptt) cc_final: 0.6683 (mptt)
REVERT: A  353 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.8032 (t160)
REVERT: B  353 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8029 (t160)
  outliers start: 9
  outliers final: 6
  residues processed: 147
  average time/residue: 0.1367
  time to fit residues: 28.4819
Evaluate side-chains
  135 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  354 MET
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0570
   chunk 36 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.0502

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.180690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.148179 restraints weight = 23385.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.155090 restraints weight = 12120.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.159824 restraints weight = 7822.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.162819 restraints weight = 5657.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.165204 restraints weight = 4454.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6798  Z= 0.142
  Angle     :  0.537   5.726   9270  Z= 0.284
  Chirality :  0.042   0.147   1080
  Planarity :  0.005   0.045   1190
  Dihedral  :  4.744  50.006    944
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.60 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 866
  helix:  1.61 (0.26), residues: 422
  sheet: -0.58 (0.58), residues: 74
  loop :  0.34 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  69 
 TYR   0.013   0.002   TYR A 369 
 PHE   0.011   0.001   PHE B 316 
 TRP   0.015   0.002   TRP B 273 
 HIS   0.004   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6796)
  covalent geometry    : angle       0.53657 ( 9266)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       1.07340 (    4)
  hydrogen bonds       : bond        0.03688 (  368)
  hydrogen bonds       : angle       4.63172 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  141 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7906 (t0) cc_final: 0.7652 (t0)
REVERT: A  353 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8109 (t160)
REVERT: B  298 ASN cc_start: 0.7960 (t0) cc_final: 0.7692 (t0)
REVERT: B  307 ASN cc_start: 0.7183 (t0) cc_final: 0.6972 (t0)
REVERT: B  375 TYR cc_start: 0.8675 (p90) cc_final: 0.8359 (p90)
  outliers start: 10
  outliers final: 5
  residues processed: 137
  average time/residue: 0.1568
  time to fit residues: 29.5953
Evaluate side-chains
  126 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 110 GLN
A 490 GLN
B 490 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.181655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.150047 restraints weight = 23155.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.158166 restraints weight = 14604.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.161709 restraints weight = 8157.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.164799 restraints weight = 5656.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.165852 restraints weight = 4528.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6798  Z= 0.112
  Angle     :  0.515   6.307   9270  Z= 0.270
  Chirality :  0.041   0.139   1080
  Planarity :  0.005   0.048   1190
  Dihedral  :  4.547  45.675    944
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.33 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.29), residues: 866
  helix:  1.83 (0.26), residues: 422
  sheet: -0.56 (0.59), residues: 74
  loop :  0.36 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  42 
 TYR   0.015   0.001   TYR A 448 
 PHE   0.010   0.001   PHE A 483 
 TRP   0.016   0.002   TRP B 273 
 HIS   0.004   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6796)
  covalent geometry    : angle       0.51515 ( 9266)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       0.86936 (    4)
  hydrogen bonds       : bond        0.03219 (  368)
  hydrogen bonds       : angle       4.39300 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  136 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7960 (t0) cc_final: 0.7682 (t0)
REVERT: A  353 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8049 (t160)
REVERT: B  298 ASN cc_start: 0.7964 (t0) cc_final: 0.7697 (t0)
REVERT: B  353 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8101 (t160)
  outliers start: 11
  outliers final: 6
  residues processed: 131
  average time/residue: 0.1513
  time to fit residues: 27.5981
Evaluate side-chains
  126 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  335 SER
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  354 MET
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
A 110 GLN
A 116 GLN
A 490 GLN
B 116 GLN
B 490 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.177609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.148319 restraints weight = 23436.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.155046 restraints weight = 13958.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.158796 restraints weight = 8330.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.160142 restraints weight = 5450.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.163141 restraints weight = 4895.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6798  Z= 0.156
  Angle     :  0.534   6.299   9270  Z= 0.282
  Chirality :  0.042   0.133   1080
  Planarity :  0.005   0.059   1190
  Dihedral  :  4.234  16.951    942
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.23 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.30), residues: 866
  helix:  1.95 (0.26), residues: 422
  sheet: -0.59 (0.59), residues: 74
  loop :  0.32 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  42 
 TYR   0.015   0.002   TYR A 448 
 PHE   0.012   0.001   PHE B 316 
 TRP   0.013   0.002   TRP A 400 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6796)
  covalent geometry    : angle       0.53340 ( 9266)
  SS BOND              : bond        0.00450 (    2)
  SS BOND              : angle       1.07075 (    4)
  hydrogen bonds       : bond        0.03227 (  368)
  hydrogen bonds       : angle       4.32737 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 MET cc_start: 0.8122 (tmm) cc_final: 0.7792 (tmm)
REVERT: A  298 ASN cc_start: 0.8036 (t0) cc_final: 0.7735 (t0)
REVERT: A  353 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8204 (t160)
REVERT: B  298 ASN cc_start: 0.7994 (t0) cc_final: 0.7692 (t0)
REVERT: B  307 ASN cc_start: 0.7212 (t0) cc_final: 0.6996 (t0)
REVERT: B  353 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8204 (t160)
  outliers start: 8
  outliers final: 5
  residues processed: 122
  average time/residue: 0.1793
  time to fit residues: 28.8856
Evaluate side-chains
  120 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  335 SER
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 26 optimal weight:    0.0370
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0870
   chunk 12 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.179886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.148819 restraints weight = 23062.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.156668 restraints weight = 14179.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.161494 restraints weight = 7567.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.164655 restraints weight = 4935.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.165718 restraints weight = 3909.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6798  Z= 0.098
  Angle     :  0.504   6.279   9270  Z= 0.260
  Chirality :  0.040   0.140   1080
  Planarity :  0.005   0.061   1190
  Dihedral  :  4.088  16.445    942
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.37 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.30), residues: 866
  helix:  2.12 (0.27), residues: 422
  sheet: -0.74 (0.58), residues: 76
  loop :  0.39 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.014   0.001   TYR A 448 
 PHE   0.013   0.001   PHE A 476 
 TRP   0.014   0.001   TRP B 273 
 HIS   0.003   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6796)
  covalent geometry    : angle       0.50392 ( 9266)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.77668 (    4)
  hydrogen bonds       : bond        0.02980 (  368)
  hydrogen bonds       : angle       4.17550 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  129 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 MET cc_start: 0.8081 (tmm) cc_final: 0.7763 (tmm)
REVERT: A  298 ASN cc_start: 0.7990 (t0) cc_final: 0.7674 (t0)
REVERT: A  353 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8118 (t160)
REVERT: B  298 ASN cc_start: 0.7938 (t0) cc_final: 0.7626 (t0)
REVERT: B  353 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8140 (t160)
  outliers start: 10
  outliers final: 7
  residues processed: 124
  average time/residue: 0.1577
  time to fit residues: 26.7196
Evaluate side-chains
  125 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  354 MET
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 47 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
A 330 GLN
A 490 GLN
B 490 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.171602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.142085 restraints weight = 23649.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.149096 restraints weight = 14758.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.150898 restraints weight = 9755.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.152912 restraints weight = 6751.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.155759 restraints weight = 5784.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   6798  Z= 0.276
  Angle     :  0.621   5.852   9270  Z= 0.335
  Chirality :  0.044   0.139   1080
  Planarity :  0.006   0.059   1190
  Dihedral  :  4.393  17.770    942
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.23 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.30), residues: 866
  helix:  1.76 (0.27), residues: 424
  sheet: -0.56 (0.59), residues: 74
  loop :  0.01 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  42 
 TYR   0.016   0.002   TYR A 369 
 PHE   0.020   0.002   PHE B 316 
 TRP   0.017   0.002   TRP A 400 
 HIS   0.003   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 6796)
  covalent geometry    : angle       0.62097 ( 9266)
  SS BOND              : bond        0.00782 (    2)
  SS BOND              : angle       1.35501 (    4)
  hydrogen bonds       : bond        0.03482 (  368)
  hydrogen bonds       : angle       4.43430 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.6710 (t0) cc_final: 0.6450 (t0)
REVERT: A  162 MET cc_start: 0.8079 (tmm) cc_final: 0.7828 (tmm)
REVERT: A  298 ASN cc_start: 0.8181 (t0) cc_final: 0.7942 (t0)
REVERT: A  333 ASN cc_start: 0.8818 (p0) cc_final: 0.8548 (p0)
REVERT: A  353 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8443 (t0)
REVERT: B  307 ASN cc_start: 0.7352 (t0) cc_final: 0.7136 (t0)
REVERT: B  353 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8367 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1900
  time to fit residues: 29.3763
Evaluate side-chains
  120 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    0.0570
   chunk 43 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 4 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 490 GLN
B 490 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.177833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.146691 restraints weight = 23128.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.154752 restraints weight = 14037.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.159072 restraints weight = 7354.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.162400 restraints weight = 4983.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.163344 restraints weight = 3948.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6798  Z= 0.106
  Angle     :  0.508   5.829   9270  Z= 0.264
  Chirality :  0.040   0.135   1080
  Planarity :  0.005   0.062   1190
  Dihedral  :  4.119  17.009    942
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.08 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.30), residues: 866
  helix:  2.08 (0.27), residues: 424
  sheet: -0.45 (0.58), residues: 74
  loop :  0.11 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  42 
 TYR   0.013   0.001   TYR A 448 
 PHE   0.009   0.001   PHE A 483 
 TRP   0.016   0.002   TRP B 273 
 HIS   0.003   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6796)
  covalent geometry    : angle       0.50753 ( 9266)
  SS BOND              : bond        0.00207 (    2)
  SS BOND              : angle       0.78191 (    4)
  hydrogen bonds       : bond        0.02959 (  368)
  hydrogen bonds       : angle       4.15658 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  131 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.6609 (t0) cc_final: 0.6385 (t0)
REVERT: A  298 ASN cc_start: 0.8011 (t0) cc_final: 0.7702 (t0)
REVERT: B  116 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7644 (mt0)
REVERT: B  353 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8180 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1658
  time to fit residues: 27.6365
Evaluate side-chains
  126 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  116 GLN
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
A 490 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.177138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.146311 restraints weight = 23226.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.155723 restraints weight = 14139.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.158746 restraints weight = 7104.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.162481 restraints weight = 4892.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.163310 restraints weight = 3756.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6798  Z= 0.113
  Angle     :  0.501   6.274   9270  Z= 0.260
  Chirality :  0.040   0.135   1080
  Planarity :  0.005   0.066   1190
  Dihedral  :  4.012  16.693    942
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 16.96 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.30), residues: 866
  helix:  2.18 (0.27), residues: 424
  sheet: -0.90 (0.55), residues: 80
  loop :  0.29 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  42 
 TYR   0.013   0.001   TYR A 448 
 PHE   0.010   0.001   PHE A 483 
 TRP   0.013   0.001   TRP B 273 
 HIS   0.002   0.001   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6796)
  covalent geometry    : angle       0.50100 ( 9266)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.83496 (    4)
  hydrogen bonds       : bond        0.02857 (  368)
  hydrogen bonds       : angle       4.09685 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.6624 (t0) cc_final: 0.6396 (t0)
REVERT: A  298 ASN cc_start: 0.8020 (t0) cc_final: 0.7696 (t0)
REVERT: B  307 ASN cc_start: 0.7206 (t0) cc_final: 0.6988 (t0)
REVERT: B  353 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8195 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 113
  average time/residue: 0.1653
  time to fit residues: 25.3456
Evaluate side-chains
  116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 80 optimal weight:    9.9990
   chunk 60 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    0.4980
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
A 490 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.178953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.147737 restraints weight = 23061.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.155555 restraints weight = 14483.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.158536 restraints weight = 8248.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.162655 restraints weight = 5778.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.163543 restraints weight = 4342.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6798  Z= 0.100
  Angle     :  0.491   5.683   9270  Z= 0.254
  Chirality :  0.040   0.135   1080
  Planarity :  0.005   0.068   1190
  Dihedral  :  3.891  16.267    942
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 17.11 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.30), residues: 866
  helix:  2.34 (0.27), residues: 424
  sheet: -1.04 (0.56), residues: 78
  loop :  0.43 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  42 
 TYR   0.012   0.001   TYR A 448 
 PHE   0.009   0.001   PHE A 483 
 TRP   0.015   0.001   TRP B 273 
 HIS   0.003   0.001   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6796)
  covalent geometry    : angle       0.49116 ( 9266)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       0.75142 (    4)
  hydrogen bonds       : bond        0.02724 (  368)
  hydrogen bonds       : angle       4.01892 ( 1134)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue VAL  412 is missing expected H atoms. Skipping.
Residue TYR  413 is missing expected H atoms. Skipping.
Residue TYR  433 is missing expected H atoms. Skipping.
Residue ILE  434 is missing expected H atoms. Skipping.
Residue ILE  435 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue ILE  491 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue ILE  494 is missing expected H atoms. Skipping.
Evaluate side-chains
  122 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.6641 (t0) cc_final: 0.6404 (t0)
REVERT: A  162 MET cc_start: 0.8099 (tmm) cc_final: 0.7838 (tmm)
REVERT: A  298 ASN cc_start: 0.7979 (t0) cc_final: 0.7659 (t0)
REVERT: B  116 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7604 (mt0)
REVERT: B  277 TRP cc_start: 0.8291 (m100) cc_final: 0.7624 (m100)
REVERT: B  353 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8122 (t160)
  outliers start: 7
  outliers final: 5
  residues processed: 119
  average time/residue: 0.1644
  time to fit residues: 26.5387
Evaluate side-chains
  119 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain B residue  116 GLN
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  353 ASN
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 10 optimal weight:    0.3980
   chunk 55 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0170
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 490 GLN
B 490 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.176561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.147042 restraints weight = 22764.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.153565 restraints weight = 11738.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.157666 restraints weight = 7443.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.160758 restraints weight = 5384.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.162667 restraints weight = 4172.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6798  Z= 0.094
  Angle     :  0.488   5.600   9270  Z= 0.251
  Chirality :  0.040   0.133   1080
  Planarity :  0.005   0.068   1190
  Dihedral  :  3.814  15.949    942
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 17.25 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.30), residues: 866
  helix:  2.42 (0.27), residues: 424
  sheet: -0.97 (0.56), residues: 78
  loop :  0.45 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  42 
 TYR   0.013   0.001   TYR A 448 
 PHE   0.009   0.001   PHE B 483 
 TRP   0.014   0.001   TRP B 273 
 HIS   0.003   0.001   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6796)
  covalent geometry    : angle       0.48801 ( 9266)
  SS BOND              : bond        0.00184 (    2)
  SS BOND              : angle       0.68547 (    4)
  hydrogen bonds       : bond        0.02683 (  368)
  hydrogen bonds       : angle       3.97279 ( 1134)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2170.51 seconds
wall clock time: 38 minutes 4.37 seconds (2284.37 seconds total)