Starting phenix.real_space_refine
on Wed Sep 17 12:56:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iny_60712/09_2025/9iny_60712.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iny_60712/09_2025/9iny_60712.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iny_60712/09_2025/9iny_60712.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iny_60712/09_2025/9iny_60712.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iny_60712/09_2025/9iny_60712.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iny_60712/09_2025/9iny_60712.cif"
  }
  resolution = 3.6
  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=  -0.005 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5532      2.51       5
     N    1461      2.21       5
     O    1776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8793
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2931
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 13, 'TRANS': 361}
    Chain: "B"
      Number of atoms: 2931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2931
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 13, 'TRANS': 361}
    Chain: "C"
      Number of atoms: 2931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2931
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 13, 'TRANS': 361}
  Time building chain proxies: 2.23, per 1000 atoms: 0.25
  Number of scatterers: 8793
  At special positions: 0
  Unit cell: (118.3, 113.1, 65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1776      8.00
     N    1461      7.00
     C    5532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 341.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 9 sheets defined
      13.8% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 100
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.779A  pdb=" N   THR A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 286
    Processing helix  chain 'A' and resid 358 through 368
    Processing helix  chain 'B' and resid 5 through 9
      removed outlier: 3.578A  pdb=" N   ASN B   8 " --> pdb=" O   LEU B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 100
      removed outlier: 3.525A  pdb=" N   TRP B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
      removed outlier: 3.522A  pdb=" N   ILE B 189 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.724A  pdb=" N   THR B 198 " --> pdb=" O   GLU B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 286
    Processing helix  chain 'B' and resid 358 through 368
    Processing helix  chain 'C' and resid 91 through 100
    Processing helix  chain 'C' and resid 185 through 190
    Processing helix  chain 'C' and resid 192 through 202
      removed outlier: 3.745A  pdb=" N   THR C 198 " --> pdb=" O   GLU C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 286
    Processing helix  chain 'C' and resid 358 through 368
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14
      removed outlier: 4.392A  pdb=" N   ILE A  11 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN A  26 " --> pdb=" O   VAL A  13 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 26 through 28
    current: chain 'A' and resid 68 through 70
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 68 through 70
    current: chain 'A' and resid 119 through 122
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 119 through 122
    current: chain 'A' and resid 145 through 159
      removed outlier: 3.935A  pdb=" N   GLN A 151 " --> pdb=" O   ASN A 172 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   SER A 170 " --> pdb=" O   ASN A 153 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   ALA A 155 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   THR A 168 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   VAL A 157 " --> pdb=" O   ARG A 166 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   ARG A 166 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 166 through 173
    current: chain 'A' and resid 220 through 221
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 220 through 221
    current: chain 'A' and resid 259 through 268
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 259 through 268
    current: chain 'A' and resid 307 through 319
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 307 through 319
    current: chain 'A' and resid 331 through 338
    Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 46
      removed outlier: 7.035A  pdb=" N   ASN A  41 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 14
      removed outlier: 4.407A  pdb=" N   ILE B  11 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN B  26 " --> pdb=" O   VAL B  13 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 26 through 28
    current: chain 'B' and resid 68 through 70
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 68 through 70
    current: chain 'B' and resid 119 through 122
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 119 through 122
    current: chain 'B' and resid 145 through 159
      removed outlier: 4.204A  pdb=" N   GLN B 151 " --> pdb=" O   ASN B 172 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   SER B 170 " --> pdb=" O   ASN B 153 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ALA B 155 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   THR B 168 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   VAL B 157 " --> pdb=" O   ARG B 166 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   ARG B 166 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 166 through 173
    current: chain 'B' and resid 220 through 221
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 220 through 221
    current: chain 'B' and resid 259 through 268
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 259 through 268
    current: chain 'B' and resid 307 through 319
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 307 through 319
    current: chain 'B' and resid 331 through 338
    Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 46
      removed outlier: 6.994A  pdb=" N   ASN B  41 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 80
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 14
      removed outlier: 4.399A  pdb=" N   ILE C  11 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN C  26 " --> pdb=" O   VAL C  13 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 26 through 28
    current: chain 'C' and resid 68 through 70
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 68 through 70
    current: chain 'C' and resid 119 through 122
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 119 through 122
    current: chain 'C' and resid 145 through 159
      removed outlier: 4.100A  pdb=" N   GLN C 151 " --> pdb=" O   ASN C 172 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   SER C 170 " --> pdb=" O   ASN C 153 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ALA C 155 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   THR C 168 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 167 through 173
    current: chain 'C' and resid 220 through 221
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 220 through 221
    current: chain 'C' and resid 259 through 268
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 259 through 268
    current: chain 'C' and resid 307 through 319
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 307 through 319
    current: chain 'C' and resid 331 through 338
    Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 46
      removed outlier: 6.971A  pdb=" N   ASN C  41 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80

    119 hydrogen bonds defined for protein.
    345 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1812
        1.33 -     1.45: 2075
        1.45 -     1.57: 5026
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 8958
  Sorted by residual:
  bond pdb=" CA  ASP C 374 "
       pdb=" CB  ASP C 374 "
    ideal  model  delta    sigma   weight residual
    1.534  1.494  0.040 1.64e-02 3.72e+03 5.85e+00
  bond pdb=" N   VAL B 376 "
       pdb=" CA  VAL B 376 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.25e-02 6.40e+03 5.13e+00
  bond pdb=" CA  SER B 354 "
       pdb=" CB  SER B 354 "
    ideal  model  delta    sigma   weight residual
    1.534  1.498  0.036 1.65e-02 3.67e+03 4.88e+00
  bond pdb=" CA  VAL B 376 "
       pdb=" C   VAL B 376 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.27e-02 6.20e+03 4.50e+00
  bond pdb=" C   SER B 354 "
       pdb=" O   SER B 354 "
    ideal  model  delta    sigma   weight residual
    1.234  1.207  0.027 1.29e-02 6.01e+03 4.44e+00
  ... (remaining 8953 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 11871
        2.09 -     4.17: 275
        4.17 -     6.26: 40
        6.26 -     8.35: 4
        8.35 -    10.44: 2
  Bond angle restraints: 12192
  Sorted by residual:
  angle pdb=" N   ALA B 375 "
        pdb=" CA  ALA B 375 "
        pdb=" C   ALA B 375 "
      ideal   model   delta    sigma   weight residual
     111.14  117.23   -6.09 1.08e+00 8.57e-01 3.18e+01
  angle pdb=" N   VAL B 376 "
        pdb=" CA  VAL B 376 "
        pdb=" C   VAL B 376 "
      ideal   model   delta    sigma   weight residual
     109.34  119.78  -10.44 2.08e+00 2.31e-01 2.52e+01
  angle pdb=" N   VAL A 376 "
        pdb=" CA  VAL A 376 "
        pdb=" C   VAL A 376 "
      ideal   model   delta    sigma   weight residual
     109.34  118.45   -9.11 2.08e+00 2.31e-01 1.92e+01
  angle pdb=" N   ALA A 375 "
        pdb=" CA  ALA A 375 "
        pdb=" C   ALA A 375 "
      ideal   model   delta    sigma   weight residual
     111.14  115.67   -4.53 1.08e+00 8.57e-01 1.76e+01
  angle pdb=" N   VAL C 376 "
        pdb=" CA  VAL C 376 "
        pdb=" C   VAL C 376 "
      ideal   model   delta    sigma   weight residual
     109.34  117.09   -7.75 2.08e+00 2.31e-01 1.39e+01
  ... (remaining 12187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.68: 4604
       12.68 -    25.36: 532
       25.36 -    38.04: 170
       38.04 -    50.72: 32
       50.72 -    63.40: 8
  Dihedral angle restraints: 5346
    sinusoidal: 2085
      harmonic: 3261
  Sorted by residual:
  dihedral pdb=" C   VAL C 376 "
           pdb=" N   VAL C 376 "
           pdb=" CA  VAL C 376 "
           pdb=" CB  VAL C 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.61   15.61     0      2.50e+00 1.60e-01 3.90e+01
  dihedral pdb=" C   VAL B 376 "
           pdb=" N   VAL B 376 "
           pdb=" CA  VAL B 376 "
           pdb=" CB  VAL B 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.34   14.34     0      2.50e+00 1.60e-01 3.29e+01
  dihedral pdb=" CA  GLY B 108 "
           pdb=" C   GLY B 108 "
           pdb=" N   THR B 109 "
           pdb=" CA  THR B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.44   28.56     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 5343 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1301
       0.098 -    0.196: 101
       0.196 -    0.295: 9
       0.295 -    0.393: 2
       0.393 -    0.491: 3
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" CA  VAL C 376 "
            pdb=" N   VAL C 376 "
            pdb=" C   VAL C 376 "
            pdb=" CB  VAL C 376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.95    0.49 2.00e-01 2.50e+01 6.02e+00
  chirality pdb=" CA  VAL B 376 "
            pdb=" N   VAL B 376 "
            pdb=" C   VAL B 376 "
            pdb=" CB  VAL B 376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.00    0.44 2.00e-01 2.50e+01 4.82e+00
  chirality pdb=" CA  ILE B 161 "
            pdb=" N   ILE B 161 "
            pdb=" C   ILE B 161 "
            pdb=" CB  ILE B 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.03    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 1413 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 160 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.20e+00
        pdb=" C   ASP B 160 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASP B 160 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE B 161 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 160 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" C   ASP C 160 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ASP C 160 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE C 161 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 161 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.80e+00
        pdb=" C   ILE B 161 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ILE B 161 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU B 162 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 39
        2.51 -     3.11: 6598
        3.11 -     3.70: 12864
        3.70 -     4.30: 19091
        4.30 -     4.90: 32117
  Nonbonded interactions: 70709
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 376 "
            pdb=" CG1 VAL A 376 "
     model   vdw
     1.909 3.460
  nonbonded pdb=" NE2 HIS C  96 "
            pdb=" O   ARG C 102 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" NE2 HIS B  96 "
            pdb=" O   ARG B 102 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OE1 GLN A 151 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG  SER B 341 "
            pdb=" OD2 ASP B 347 "
     model   vdw
     2.299 3.040
  ... (remaining 70704 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'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.040
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
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   0.040   8958  Z= 0.196
  Angle     :  0.751  10.435  12192  Z= 0.442
  Chirality :  0.055   0.491   1416
  Planarity :  0.003   0.041   1578
  Dihedral  : 12.392  63.401   3252
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  7.24 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  0.10 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.25), residues: 1119
  helix:  0.56 (0.46), residues: 126
  sheet: -0.74 (0.26), residues: 450
  loop : -2.26 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  53 
 TYR   0.021   0.001   TYR B 357 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.016   0.001   TRP A 144 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8958)
  covalent geometry    : angle       0.75096 (12192)
  hydrogen bonds       : bond        0.21292 (  119)
  hydrogen bonds       : angle       7.16441 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.5999 (ptt) cc_final: 0.5769 (ptt)
REVERT: C  210 ILE cc_start: 0.8288 (tt) cc_final: 0.7982 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 71
  average time/residue: 0.0645
  time to fit residues: 7.3909
Evaluate side-chains
  49 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  354 SER
Chi-restraints excluded: chain C residue  161 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.1980
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    0.0980
   overall best weight:    4.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 182 GLN
B 113 HIS
B 115 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.115448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103646 restraints weight = 13350.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.105003 restraints weight = 9542.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.105423 restraints weight = 8615.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.105933 restraints weight = 7158.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.106367 restraints weight = 6356.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8958  Z= 0.263
  Angle     :  0.709   7.382  12192  Z= 0.378
  Chirality :  0.049   0.186   1416
  Planarity :  0.004   0.039   1578
  Dihedral  :  6.441  57.647   1206
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  8.31 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  5.57 %
    Favored  : 93.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.47 (0.24), residues: 1119
  helix: -0.15 (0.40), residues: 129
  sheet: -1.09 (0.26), residues: 438
  loop : -2.49 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  53 
 TYR   0.023   0.002   TYR B 239 
 PHE   0.015   0.002   PHE C 259 
 TRP   0.012   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 8958)
  covalent geometry    : angle       0.70857 (12192)
  hydrogen bonds       : bond        0.04615 (  119)
  hydrogen bonds       : angle       5.73743 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  120 MET cc_start: 0.6803 (ptt) cc_final: 0.6162 (ptt)
REVERT: B  342 ASP cc_start: 0.5930 (t0) cc_final: 0.5676 (t0)
REVERT: C  126 ASN cc_start: 0.8152 (t0) cc_final: 0.7915 (p0)
  outliers start: 13
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0581
  time to fit residues: 5.6657
Evaluate side-chains
  46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 182 GLN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.105420 restraints weight = 13169.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107033 restraints weight = 9439.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107522 restraints weight = 7825.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108110 restraints weight = 6596.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108248 restraints weight = 5933.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8958  Z= 0.170
  Angle     :  0.603   6.809  12192  Z= 0.321
  Chirality :  0.047   0.317   1416
  Planarity :  0.003   0.032   1578
  Dihedral  :  5.816  43.121   1204
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  7.69 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.92 %
    Favored  : 89.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.49 (0.23), residues: 1119
  helix: -0.12 (0.41), residues: 129
  sheet: -1.23 (0.26), residues: 405
  loop : -2.35 (0.22), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  53 
 TYR   0.013   0.001   TYR B 239 
 PHE   0.012   0.001   PHE B  72 
 TRP   0.008   0.001   TRP C  36 
 HIS   0.005   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8958)
  covalent geometry    : angle       0.60297 (12192)
  hydrogen bonds       : bond        0.03857 (  119)
  hydrogen bonds       : angle       5.40541 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.6653 (ptt) cc_final: 0.6068 (ptt)
REVERT: B  342 ASP cc_start: 0.5773 (t0) cc_final: 0.5520 (t0)
REVERT: C  126 ASN cc_start: 0.8107 (t0) cc_final: 0.7879 (p0)
  outliers start: 12
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0511
  time to fit residues: 4.9234
Evaluate side-chains
  50 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 96 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 83 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0060
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.3400

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 114 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.116767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104261 restraints weight = 13330.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.106231 restraints weight = 9093.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107784 restraints weight = 6921.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108873 restraints weight = 5567.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.109623 restraints weight = 4696.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8958  Z= 0.157
  Angle     :  0.579   6.786  12192  Z= 0.307
  Chirality :  0.047   0.339   1416
  Planarity :  0.003   0.031   1578
  Dihedral  :  5.675  44.377   1204
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  8.04 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.64 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.23), residues: 1119
  helix: -0.04 (0.42), residues: 129
  sheet: -1.27 (0.26), residues: 390
  loop : -2.34 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  56 
 TYR   0.012   0.001   TYR B 350 
 PHE   0.011   0.001   PHE B  72 
 TRP   0.011   0.001   TRP A 169 
 HIS   0.004   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8958)
  covalent geometry    : angle       0.57922 (12192)
  hydrogen bonds       : bond        0.03380 (  119)
  hydrogen bonds       : angle       5.28394 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.6792 (ptt) cc_final: 0.6119 (ptt)
REVERT: B  342 ASP cc_start: 0.5628 (t0) cc_final: 0.5420 (t0)
REVERT: C  210 ILE cc_start: 0.8463 (tt) cc_final: 0.8122 (tt)
  outliers start: 15
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0592
  time to fit residues: 6.1834
Evaluate side-chains
  46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 104 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.119930 restraints weight = 13455.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.122254 restraints weight = 8789.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.123875 restraints weight = 6401.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.124865 restraints weight = 5030.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125722 restraints weight = 4209.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8958  Z= 0.129
  Angle     :  0.554   6.423  12192  Z= 0.293
  Chirality :  0.045   0.293   1416
  Planarity :  0.003   0.030   1578
  Dihedral  :  5.492  45.445   1204
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  6.70 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.87 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.23), residues: 1119
  helix:  0.13 (0.43), residues: 129
  sheet: -1.18 (0.26), residues: 414
  loop : -2.49 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  56 
 TYR   0.011   0.001   TYR B 350 
 PHE   0.011   0.001   PHE B  72 
 TRP   0.009   0.001   TRP A 169 
 HIS   0.003   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8958)
  covalent geometry    : angle       0.55413 (12192)
  hydrogen bonds       : bond        0.03145 (  119)
  hydrogen bonds       : angle       5.16175 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: C  210 ILE cc_start: 0.8160 (tt) cc_final: 0.7877 (tt)
  outliers start: 13
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0563
  time to fit residues: 5.8508
Evaluate side-chains
  50 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  161 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0570
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 ASN
** C  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117557 restraints weight = 13560.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.119784 restraints weight = 9027.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.121354 restraints weight = 6700.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.122478 restraints weight = 5317.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.123201 restraints weight = 4425.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8958  Z= 0.182
  Angle     :  0.590   6.577  12192  Z= 0.312
  Chirality :  0.046   0.251   1416
  Planarity :  0.003   0.030   1578
  Dihedral  :  5.589  44.940   1204
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  8.13 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.07 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.60 (0.23), residues: 1119
  helix:  0.01 (0.42), residues: 129
  sheet: -1.24 (0.25), residues: 408
  loop : -2.55 (0.22), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  56 
 TYR   0.012   0.001   TYR B 239 
 PHE   0.011   0.002   PHE A 259 
 TRP   0.009   0.001   TRP A 169 
 HIS   0.004   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8958)
  covalent geometry    : angle       0.58982 (12192)
  hydrogen bonds       : bond        0.03337 (  119)
  hydrogen bonds       : angle       5.24258 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 41
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8520 (t0)
REVERT: A  232 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8039 (p)
REVERT: B  232 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8097 (p)
REVERT: C  210 ILE cc_start: 0.8294 (tt) cc_final: 0.8008 (tt)
  outliers start: 21
  outliers final: 12
  residues processed: 58
  average time/residue: 0.0589
  time to fit residues: 5.7032
Evaluate side-chains
  54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 109 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 36 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 37 optimal weight:    0.3980
   chunk 102 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 ASN
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.131150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.118404 restraints weight = 13551.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.120643 restraints weight = 9004.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.122216 restraints weight = 6658.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.123325 restraints weight = 5270.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.124057 restraints weight = 4379.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8958  Z= 0.149
  Angle     :  0.566   6.299  12192  Z= 0.300
  Chirality :  0.045   0.239   1416
  Planarity :  0.003   0.029   1578
  Dihedral  :  5.517  45.360   1204
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  7.60 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.48 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.62 (0.23), residues: 1119
  helix:  0.09 (0.43), residues: 129
  sheet: -1.32 (0.25), residues: 414
  loop : -2.54 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  56 
 TYR   0.011   0.001   TYR B 350 
 PHE   0.011   0.001   PHE B  72 
 TRP   0.010   0.001   TRP A 169 
 HIS   0.015   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8958)
  covalent geometry    : angle       0.56597 (12192)
  hydrogen bonds       : bond        0.03203 (  119)
  hydrogen bonds       : angle       5.18134 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8483 (t0)
REVERT: A  232 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8106 (p)
REVERT: B  277 MET cc_start: 0.8498 (tpt) cc_final: 0.7829 (tpt)
REVERT: C  210 ILE cc_start: 0.8222 (tt) cc_final: 0.7908 (tt)
REVERT: C  231 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7408 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 54
  average time/residue: 0.0714
  time to fit residues: 6.3608
Evaluate side-chains
  56 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  206 ASN
Chi-restraints excluded: chain C residue  231 PHE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  313 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 75 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 ASN
** B  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.125178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.112064 restraints weight = 13657.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.113434 restraints weight = 9355.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.114315 restraints weight = 7678.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.114575 restraints weight = 6689.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.115730 restraints weight = 6151.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   8958  Z= 0.261
  Angle     :  0.659   6.730  12192  Z= 0.349
  Chirality :  0.048   0.232   1416
  Planarity :  0.004   0.032   1578
  Dihedral  :  5.862  44.367   1204
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.20 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.07 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.84 (0.23), residues: 1119
  helix: -0.22 (0.41), residues: 129
  sheet: -1.52 (0.26), residues: 387
  loop : -2.56 (0.22), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  56 
 TYR   0.018   0.002   TYR B 239 
 PHE   0.012   0.002   PHE B 259 
 TRP   0.014   0.002   TRP A 169 
 HIS   0.011   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 8958)
  covalent geometry    : angle       0.65911 (12192)
  hydrogen bonds       : bond        0.03712 (  119)
  hydrogen bonds       : angle       5.41014 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 37
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8618 (t0)
REVERT: A  232 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8203 (p)
REVERT: A  299 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8442 (mp)
REVERT: B  231 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7356 (t80)
REVERT: B  232 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8247 (p)
REVERT: C   93 MET cc_start: 0.7692 (mtm) cc_final: 0.7229 (mtm)
REVERT: C  210 ILE cc_start: 0.8471 (tt) cc_final: 0.8201 (tt)
REVERT: C  231 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7470 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 60
  average time/residue: 0.0606
  time to fit residues: 6.1389
Evaluate side-chains
  58 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 35
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  231 PHE
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  231 PHE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 114 ASN
A 118 ASN
** B  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.130818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117562 restraints weight = 13521.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.119928 restraints weight = 8717.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121598 restraints weight = 6380.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.122774 restraints weight = 5019.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.123663 restraints weight = 4146.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8958  Z= 0.127
  Angle     :  0.556   6.096  12192  Z= 0.294
  Chirality :  0.045   0.223   1416
  Planarity :  0.003   0.031   1578
  Dihedral  :  5.532  46.044   1204
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  6.43 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.88 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.23), residues: 1119
  helix:  0.12 (0.43), residues: 129
  sheet: -1.37 (0.26), residues: 378
  loop : -2.53 (0.22), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  56 
 TYR   0.012   0.001   TYR A 357 
 PHE   0.010   0.001   PHE B  72 
 TRP   0.012   0.001   TRP A 169 
 HIS   0.006   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8958)
  covalent geometry    : angle       0.55613 (12192)
  hydrogen bonds       : bond        0.03026 (  119)
  hydrogen bonds       : angle       5.16580 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8606 (t0)
REVERT: A  299 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8198 (mp)
REVERT: B  126 ASN cc_start: 0.8715 (p0) cc_final: 0.8500 (p0)
REVERT: B  277 MET cc_start: 0.8494 (tpt) cc_final: 0.7863 (tpt)
REVERT: C   93 MET cc_start: 0.7679 (mtm) cc_final: 0.7444 (mtm)
REVERT: C  210 ILE cc_start: 0.8270 (tt) cc_final: 0.7977 (tt)
REVERT: C  231 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7407 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 62
  average time/residue: 0.0658
  time to fit residues: 6.6821
Evaluate side-chains
  55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  231 PHE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0870
   chunk 63 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    4.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 ASN
** B  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.124738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.111575 restraints weight = 13625.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.112864 restraints weight = 9428.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.113671 restraints weight = 7766.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.114186 restraints weight = 6926.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.114850 restraints weight = 6207.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   8958  Z= 0.262
  Angle     :  0.658   7.363  12192  Z= 0.347
  Chirality :  0.047   0.219   1416
  Planarity :  0.004   0.032   1578
  Dihedral  :  5.822  44.978   1204
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  9.83 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.78 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.91 (0.23), residues: 1119
  helix: -0.16 (0.42), residues: 129
  sheet: -1.47 (0.25), residues: 402
  loop : -2.75 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  56 
 TYR   0.018   0.002   TYR B 239 
 PHE   0.012   0.002   PHE A 259 
 TRP   0.016   0.002   TRP A 169 
 HIS   0.005   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 8958)
  covalent geometry    : angle       0.65843 (12192)
  hydrogen bonds       : bond        0.03574 (  119)
  hydrogen bonds       : angle       5.36238 (  345)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 32
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8635 (t0)
REVERT: A  232 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8221 (p)
REVERT: A  299 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8504 (mp)
REVERT: B  231 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7557 (t80)
REVERT: C  210 ILE cc_start: 0.8476 (tt) cc_final: 0.8207 (tt)
REVERT: C  231 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7568 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 53
  average time/residue: 0.0563
  time to fit residues: 5.0755
Evaluate side-chains
  52 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 32
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  231 PHE
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  231 PHE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  323 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 24 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0270
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.133852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.121041 restraints weight = 13421.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.123429 restraints weight = 8566.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.125080 restraints weight = 6193.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.126197 restraints weight = 4848.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.126964 restraints weight = 4005.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8958  Z= 0.102
  Angle     :  0.532   6.089  12192  Z= 0.283
  Chirality :  0.044   0.210   1416
  Planarity :  0.003   0.028   1578
  Dihedral  :  5.371  47.681   1204
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  5.45 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.59 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.61 (0.23), residues: 1119
  helix:  0.37 (0.44), residues: 129
  sheet: -1.35 (0.25), residues: 390
  loop : -2.53 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  56 
 TYR   0.012   0.001   TYR B  92 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8958)
  covalent geometry    : angle       0.53173 (12192)
  hydrogen bonds       : bond        0.02855 (  119)
  hydrogen bonds       : angle       5.08148 (  345)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1112.79 seconds
wall clock time: 20 minutes 13.21 seconds (1213.21 seconds total)