Starting phenix.real_space_refine
on Sat Aug 23 11:42:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x82_38133/08_2025/8x82_38133_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x82_38133/08_2025/8x82_38133.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x82_38133/08_2025/8x82_38133.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x82_38133/08_2025/8x82_38133.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x82_38133/08_2025/8x82_38133_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x82_38133/08_2025/8x82_38133_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      72      5.16       5
     C    7796      2.51       5
     N    2048      2.21       5
     O    2088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12004
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3001
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 6, 'TRANS': 373}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.23, per 1000 atoms: 0.19
  Number of scatterers: 12004
  At special positions: 0
  Unit cell: (108.81, 108.81, 105.09, 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      72     16.00
     O    2088      8.00
     N    2048      7.00
     C    7796      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: 1.05
  Conformation dependent library (CDL) restraints added in 716.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2896

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      85.3% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 37 through 64
    Processing helix  chain 'A' and resid 73 through 100
      removed outlier: 3.603A  pdb=" N   VAL A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 119
    Processing helix  chain 'A' and resid 120 through 123
      removed outlier: 3.539A  pdb=" N   ASN A 123 " --> pdb=" O   ASN A 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 120 through 123'
    Processing helix  chain 'A' and resid 124 through 162
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.534A  pdb=" N   VAL A 172 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 215
    Processing helix  chain 'A' and resid 263 through 321
      removed outlier: 6.049A  pdb=" N   ILE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   ALA A 295 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 357
      Proline residue:  A 347  - end of helix
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 371 through 387
      removed outlier: 4.207A  pdb=" N   VAL A 387 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 425
      removed outlier: 3.651A  pdb=" N   THR A 406 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 17
    Processing helix  chain 'B' and resid 37 through 64
    Processing helix  chain 'B' and resid 73 through 100
      removed outlier: 3.603A  pdb=" N   VAL B  87 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 119
    Processing helix  chain 'B' and resid 120 through 123
      removed outlier: 3.539A  pdb=" N   ASN B 123 " --> pdb=" O   ASN B 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 120 through 123'
    Processing helix  chain 'B' and resid 124 through 162
    Processing helix  chain 'B' and resid 168 through 174
      removed outlier: 3.534A  pdb=" N   VAL B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 215
    Processing helix  chain 'B' and resid 263 through 321
      removed outlier: 6.049A  pdb=" N   ILE B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   ALA B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 357
      Proline residue:  B 347  - end of helix
    Processing helix  chain 'B' and resid 357 through 369
    Processing helix  chain 'B' and resid 371 through 387
      removed outlier: 4.207A  pdb=" N   VAL B 387 " --> pdb=" O   GLN B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 425
      removed outlier: 3.652A  pdb=" N   THR B 406 " --> pdb=" O   ARG B 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 17
    Processing helix  chain 'C' and resid 37 through 64
    Processing helix  chain 'C' and resid 73 through 100
      removed outlier: 3.603A  pdb=" N   VAL C  87 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 119
    Processing helix  chain 'C' and resid 120 through 123
      removed outlier: 3.539A  pdb=" N   ASN C 123 " --> pdb=" O   ASN C 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 120 through 123'
    Processing helix  chain 'C' and resid 124 through 162
    Processing helix  chain 'C' and resid 168 through 174
      removed outlier: 3.534A  pdb=" N   VAL C 172 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 215
    Processing helix  chain 'C' and resid 263 through 321
      removed outlier: 6.049A  pdb=" N   ILE C 294 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   ALA C 295 " --> pdb=" O   SER C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 324 through 357
      Proline residue:  C 347  - end of helix
    Processing helix  chain 'C' and resid 357 through 369
    Processing helix  chain 'C' and resid 371 through 387
      removed outlier: 4.207A  pdb=" N   VAL C 387 " --> pdb=" O   GLN C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 425
      removed outlier: 3.651A  pdb=" N   THR C 406 " --> pdb=" O   ARG C 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 17
    Processing helix  chain 'D' and resid 37 through 64
    Processing helix  chain 'D' and resid 73 through 100
      removed outlier: 3.603A  pdb=" N   VAL D  87 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 119
    Processing helix  chain 'D' and resid 120 through 123
      removed outlier: 3.539A  pdb=" N   ASN D 123 " --> pdb=" O   ASN D 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 120 through 123'
    Processing helix  chain 'D' and resid 124 through 162
    Processing helix  chain 'D' and resid 168 through 174
      removed outlier: 3.534A  pdb=" N   VAL D 172 " --> pdb=" O   THR D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 215
    Processing helix  chain 'D' and resid 263 through 321
      removed outlier: 6.049A  pdb=" N   ILE D 294 " --> pdb=" O   ASN D 290 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   ALA D 295 " --> pdb=" O   SER D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 357
      Proline residue:  D 347  - end of helix
    Processing helix  chain 'D' and resid 357 through 369
    Processing helix  chain 'D' and resid 371 through 387
      removed outlier: 4.207A  pdb=" N   VAL D 387 " --> pdb=" O   GLN D 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 402 through 425
      removed outlier: 3.651A  pdb=" N   THR D 406 " --> pdb=" O   ARG D 402 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26
      removed outlier: 3.527A  pdb=" N   VAL A  25 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393
      removed outlier: 4.511A  pdb=" N   PHE A 392 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26
      removed outlier: 3.527A  pdb=" N   VAL B  25 " --> pdb=" O   GLU B  33 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393
      removed outlier: 4.511A  pdb=" N   PHE B 392 " --> pdb=" O   VAL B 400 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26
      removed outlier: 3.527A  pdb=" N   VAL C  25 " --> pdb=" O   GLU C  33 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393
      removed outlier: 4.511A  pdb=" N   PHE C 392 " --> pdb=" O   VAL C 400 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26
      removed outlier: 3.527A  pdb=" N   VAL D  25 " --> pdb=" O   GLU D  33 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393
      removed outlier: 4.511A  pdb=" N   PHE D 392 " --> pdb=" O   VAL D 400 " (cutoff:3.500A)

    1068 hydrogen bonds defined for protein.
    3204 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: 2.33

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3790
        1.34 -     1.46: 2718
        1.46 -     1.58: 5616
        1.58 -     1.69: 0
        1.69 -     1.81: 112
  Bond restraints: 12236
  Sorted by residual:
  bond pdb=" CA  ILE A 176 "
       pdb=" C   ILE A 176 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.009 8.80e-03 1.29e+04 9.99e-01
  bond pdb=" CA  ILE B 176 "
       pdb=" C   ILE B 176 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.009 8.80e-03 1.29e+04 9.99e-01
  bond pdb=" C   ILE B  67 "
       pdb=" O   ILE B  67 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.009 1.01e-02 9.80e+03 7.92e-01
  bond pdb=" C   ILE D  67 "
       pdb=" O   ILE D  67 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.009 1.01e-02 9.80e+03 7.92e-01
  bond pdb=" C   ILE D 176 "
       pdb=" N   PRO D 177 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.36e-01
  ... (remaining 12231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 16165
        1.00 -     2.00: 338
        2.00 -     3.01: 63
        3.01 -     4.01: 18
        4.01 -     5.01: 12
  Bond angle restraints: 16596
  Sorted by residual:
  angle pdb=" C   TYR B 175 "
        pdb=" N   ILE B 176 "
        pdb=" CA  ILE B 176 "
      ideal   model   delta    sigma   weight residual
     120.24  123.00   -2.76 6.30e-01 2.52e+00 1.91e+01
  angle pdb=" C   TYR A 175 "
        pdb=" N   ILE A 176 "
        pdb=" CA  ILE A 176 "
      ideal   model   delta    sigma   weight residual
     120.24  123.00   -2.76 6.30e-01 2.52e+00 1.91e+01
  angle pdb=" C   TYR C 175 "
        pdb=" N   ILE C 176 "
        pdb=" CA  ILE C 176 "
      ideal   model   delta    sigma   weight residual
     120.33  123.03   -2.70 8.00e-01 1.56e+00 1.14e+01
  angle pdb=" C   TYR D 175 "
        pdb=" N   ILE D 176 "
        pdb=" CA  ILE D 176 "
      ideal   model   delta    sigma   weight residual
     120.33  123.03   -2.70 8.00e-01 1.56e+00 1.14e+01
  angle pdb=" C   VAL D 345 "
        pdb=" N   GLU D 346 "
        pdb=" CA  GLU D 346 "
      ideal   model   delta    sigma   weight residual
     120.26  124.12   -3.86 1.34e+00 5.57e-01 8.31e+00
  ... (remaining 16591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 6284
       17.10 -    34.21: 712
       34.21 -    51.31: 200
       51.31 -    68.42: 32
       68.42 -    85.52: 24
  Dihedral angle restraints: 7252
    sinusoidal: 2792
      harmonic: 4460
  Sorted by residual:
  dihedral pdb=" CA  ASP B 276 "
           pdb=" CB  ASP B 276 "
           pdb=" CG  ASP B 276 "
           pdb=" OD1 ASP B 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.04   58.04     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  ASP D 276 "
           pdb=" CB  ASP D 276 "
           pdb=" CG  ASP D 276 "
           pdb=" OD1 ASP D 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.99   57.99     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  ASP A 276 "
           pdb=" CB  ASP A 276 "
           pdb=" CG  ASP A 276 "
           pdb=" OD1 ASP A 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.99   57.99     1      2.00e+01 2.50e-03 1.13e+01
  ... (remaining 7249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 1210
       0.024 -    0.047: 470
       0.047 -    0.071: 244
       0.071 -    0.095: 37
       0.095 -    0.119: 27
  Chirality restraints: 1988
  Sorted by residual:
  chirality pdb=" CA  ILE A 163 "
            pdb=" N   ILE A 163 "
            pdb=" C   ILE A 163 "
            pdb=" CB  ILE A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.51e-01
  chirality pdb=" CA  ILE C 163 "
            pdb=" N   ILE C 163 "
            pdb=" C   ILE C 163 "
            pdb=" CB  ILE C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  ILE D 163 "
            pdb=" N   ILE D 163 "
            pdb=" C   ILE D 163 "
            pdb=" CB  ILE D 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 1985 not shown)

  Planarity restraints: 2032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 176 "    0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO B 177 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 177 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 177 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 176 "    0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO A 177 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 177 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 177 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 176 "   -0.017 5.00e-02 4.00e+02   2.50e-02 1.00e+00
        pdb=" N   PRO C 177 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO C 177 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 177 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 2029 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 284
        2.72 -     3.27: 12504
        3.27 -     3.81: 21460
        3.81 -     4.36: 23941
        4.36 -     4.90: 42851
  Nonbonded interactions: 101040
  Sorted by model distance:
  nonbonded pdb=" O   ALA D  81 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ALA A  81 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ALA C  81 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ALA B  81 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OD1 ASN A 207 "
            pdb=" OG1 THR A 358 "
     model   vdw
     2.244 3.040
  ... (remaining 101035 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.680
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
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      :  0.002   0.025  12236  Z= 0.105
  Angle     :  0.408   5.012  16596  Z= 0.260
  Chirality :  0.033   0.119   1988
  Planarity :  0.002   0.025   2032
  Dihedral  : 16.428  85.523   4356
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 18.12 %
    Favored  : 81.04 %
  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:  3.68 (0.21), residues: 1504
  helix:  3.02 (0.13), residues: 1248
  sheet:  1.67 (0.77), residues: 48
  loop : -1.49 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 156 
 TYR   0.005   0.001   TYR B 415 
 PHE   0.007   0.001   PHE B 178 
 TRP   0.007   0.001   TRP D 154 
 HIS   0.002   0.001   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (12236)
  covalent geometry    : angle       0.40818 (16596)
  hydrogen bonds       : bond        0.10060 ( 1068)
  hydrogen bonds       : angle       4.81661 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 180
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6565 (mmm160) cc_final: 0.5840 (mtm110)
REVERT: A  129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7061 (ttm170)
REVERT: A  131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5478 (tmt-80)
REVERT: A  272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5990 (ttpp)
REVERT: A  279 GLU cc_start: 0.8121 (tt0) cc_final: 0.7790 (tt0)
REVERT: A  367 ARG cc_start: 0.6379 (mtm-85) cc_final: 0.6145 (mtm-85)
REVERT: A  399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7120 (tpt170)
REVERT: B  126 ARG cc_start: 0.6536 (mmm160) cc_final: 0.5802 (mtm110)
REVERT: B  129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170)
REVERT: B  131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5481 (tmt-80)
REVERT: B  272 LYS cc_start: 0.6761 (tppp) cc_final: 0.5993 (ttpp)
REVERT: B  279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0)
REVERT: B  399 ARG cc_start: 0.7769 (mtm180) cc_final: 0.7140 (tpt170)
REVERT: C  126 ARG cc_start: 0.6535 (mmm160) cc_final: 0.5800 (mtm110)
REVERT: C  129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170)
REVERT: C  131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80)
REVERT: C  272 LYS cc_start: 0.6743 (tppp) cc_final: 0.5988 (ttpp)
REVERT: C  279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0)
REVERT: C  399 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7175 (tpt170)
REVERT: D  126 ARG cc_start: 0.6563 (mmm160) cc_final: 0.5840 (mtm110)
REVERT: D  129 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7061 (ttm170)
REVERT: D  131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80)
REVERT: D  272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5985 (ttpp)
REVERT: D  279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7716 (tt0)
REVERT: D  399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7137 (tpt170)
  outliers start: 11
  outliers final: 0
  residues processed: 191
  average time/residue: 0.6462
  time to fit residues: 132.0807
Evaluate side-chains
  136 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 383 GLN
A 421 GLN
A 423 GLN
B 189 GLN
B 383 GLN
B 421 GLN
B 423 GLN
C 189 GLN
C 383 GLN
C 421 GLN
C 423 GLN
D 189 GLN
D 383 GLN
D 421 GLN
D 423 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.162372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118245 restraints weight = 12093.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.62
r_work: 0.3056 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12236  Z= 0.131
  Angle     :  0.422   4.797  16596  Z= 0.234
  Chirality :  0.035   0.131   1988
  Planarity :  0.003   0.026   2032
  Dihedral  :  3.346  11.757   1656
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.36 %
    Favored  : 80.73 %
  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:  3.58 (0.21), residues: 1504
  helix:  2.88 (0.13), residues: 1260
  sheet:  1.67 (0.76), residues: 48
  loop : -1.24 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 367 
 TYR   0.010   0.001   TYR B 175 
 PHE   0.011   0.002   PHE A  11 
 TRP   0.005   0.001   TRP D 154 
 HIS   0.002   0.001   HIS C 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (12236)
  covalent geometry    : angle       0.42237 (16596)
  hydrogen bonds       : bond        0.04437 ( 1068)
  hydrogen bonds       : angle       4.02042 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7329 (mtm110) cc_final: 0.6616 (mtm110)
REVERT: A  131 ARG cc_start: 0.7709 (mpt-90) cc_final: 0.6236 (tmt-80)
REVERT: A  272 LYS cc_start: 0.7261 (tppp) cc_final: 0.6652 (ttpp)
REVERT: A  279 GLU cc_start: 0.8456 (tt0) cc_final: 0.8201 (tt0)
REVERT: A  399 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7642 (tpt170)
REVERT: B  126 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6627 (mtm110)
REVERT: B  131 ARG cc_start: 0.7706 (mpt-90) cc_final: 0.6230 (tmt-80)
REVERT: B  272 LYS cc_start: 0.7269 (tppp) cc_final: 0.6661 (ttpp)
REVERT: B  279 GLU cc_start: 0.8451 (tt0) cc_final: 0.8198 (tt0)
REVERT: B  399 ARG cc_start: 0.8401 (mtm180) cc_final: 0.7655 (tpt170)
REVERT: C  126 ARG cc_start: 0.7331 (mtm110) cc_final: 0.6621 (mtm110)
REVERT: C  131 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.6232 (tmt-80)
REVERT: C  272 LYS cc_start: 0.7266 (tppp) cc_final: 0.6656 (ttpp)
REVERT: C  279 GLU cc_start: 0.8456 (tt0) cc_final: 0.8202 (tt0)
REVERT: C  391 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6824 (m-30)
REVERT: C  399 ARG cc_start: 0.8399 (mtm180) cc_final: 0.7654 (tpt170)
REVERT: D  126 ARG cc_start: 0.7335 (mtm110) cc_final: 0.6626 (mtm110)
REVERT: D  131 ARG cc_start: 0.7712 (mpt-90) cc_final: 0.6241 (tmt-80)
REVERT: D  272 LYS cc_start: 0.7264 (tppp) cc_final: 0.6654 (ttpp)
REVERT: D  391 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6835 (m-30)
REVERT: D  399 ARG cc_start: 0.8416 (mtm180) cc_final: 0.7656 (tpt170)
  outliers start: 38
  outliers final: 8
  residues processed: 157
  average time/residue: 0.6474
  time to fit residues: 109.4231
Evaluate side-chains
  148 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue  391 ASP
Chi-restraints excluded: chain D residue  404 ILE
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0870
   chunk 92 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 146 optimal weight:    5.9990
   chunk 149 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 383 GLN
B 189 GLN
B 383 GLN
C 189 GLN
C 383 GLN
D 189 GLN
D 383 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.157641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.113237 restraints weight = 12115.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.62
r_work: 0.3041 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12236  Z= 0.184
  Angle     :  0.473   5.183  16596  Z= 0.259
  Chirality :  0.037   0.129   1988
  Planarity :  0.003   0.025   2032
  Dihedral  :  3.557  12.825   1656
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.74 %
    Favored  : 79.82 %
  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:  3.17 (0.21), residues: 1504
  helix:  2.59 (0.13), residues: 1264
  sheet:  1.21 (0.72), residues: 48
  loop : -1.28 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 424 
 TYR   0.015   0.001   TYR B 175 
 PHE   0.012   0.002   PHE C  11 
 TRP   0.006   0.001   TRP B 174 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (12236)
  covalent geometry    : angle       0.47268 (16596)
  hydrogen bonds       : bond        0.04789 ( 1068)
  hydrogen bonds       : angle       4.11531 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.8104 (p) cc_final: 0.7880 (m)
REVERT: A   33 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7632 (mt-10)
REVERT: A  114 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7151 (mtmt)
REVERT: A  126 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6307 (mtm110)
REVERT: A  131 ARG cc_start: 0.7622 (mpt-90) cc_final: 0.6054 (tmt-80)
REVERT: A  272 LYS cc_start: 0.7319 (tppp) cc_final: 0.6694 (ttpp)
REVERT: A  279 GLU cc_start: 0.8457 (tt0) cc_final: 0.8166 (tt0)
REVERT: A  313 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6428 (m-10)
REVERT: A  331 MET cc_start: 0.7003 (ttp) cc_final: 0.6728 (ttp)
REVERT: A  380 LYS cc_start: 0.7426 (mmtp) cc_final: 0.7014 (mmmt)
REVERT: A  399 ARG cc_start: 0.8404 (mtm180) cc_final: 0.7522 (tpt170)
REVERT: B   25 VAL cc_start: 0.8099 (p) cc_final: 0.7875 (m)
REVERT: B   33 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7631 (mt-10)
REVERT: B  114 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7138 (mtmt)
REVERT: B  126 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6305 (mtm110)
REVERT: B  131 ARG cc_start: 0.7620 (mpt-90) cc_final: 0.6058 (tmt-80)
REVERT: B  272 LYS cc_start: 0.7318 (tppp) cc_final: 0.6694 (ttpp)
REVERT: B  279 GLU cc_start: 0.8441 (tt0) cc_final: 0.8151 (tt0)
REVERT: B  313 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6439 (m-10)
REVERT: B  331 MET cc_start: 0.6993 (ttp) cc_final: 0.6718 (ttp)
REVERT: B  380 LYS cc_start: 0.7429 (mmtp) cc_final: 0.7019 (mmmt)
REVERT: B  399 ARG cc_start: 0.8406 (mtm180) cc_final: 0.7522 (tpt170)
REVERT: C   25 VAL cc_start: 0.8106 (p) cc_final: 0.7885 (m)
REVERT: C   33 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7625 (mt-10)
REVERT: C  114 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7143 (mtmt)
REVERT: C  126 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6312 (mtm110)
REVERT: C  131 ARG cc_start: 0.7628 (mpt-90) cc_final: 0.6071 (tmt-80)
REVERT: C  272 LYS cc_start: 0.7340 (tppp) cc_final: 0.6714 (ttpp)
REVERT: C  279 GLU cc_start: 0.8442 (tt0) cc_final: 0.8153 (tt0)
REVERT: C  313 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6417 (m-10)
REVERT: C  331 MET cc_start: 0.7012 (ttp) cc_final: 0.6735 (ttp)
REVERT: C  380 LYS cc_start: 0.7426 (mmtp) cc_final: 0.7018 (mmmt)
REVERT: C  399 ARG cc_start: 0.8408 (mtm180) cc_final: 0.7529 (tpt170)
REVERT: D   25 VAL cc_start: 0.8109 (p) cc_final: 0.7886 (m)
REVERT: D   33 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7649 (mt-10)
REVERT: D  114 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7155 (mtmt)
REVERT: D  126 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6293 (mtm110)
REVERT: D  131 ARG cc_start: 0.7627 (mpt-90) cc_final: 0.6063 (tmt-80)
REVERT: D  272 LYS cc_start: 0.7340 (tppp) cc_final: 0.6713 (ttpp)
REVERT: D  313 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6441 (m-10)
REVERT: D  331 MET cc_start: 0.7004 (ttp) cc_final: 0.6726 (ttp)
REVERT: D  380 LYS cc_start: 0.7406 (mmtp) cc_final: 0.6992 (mmmt)
REVERT: D  399 ARG cc_start: 0.8415 (mtm180) cc_final: 0.7528 (tpt170)
  outliers start: 32
  outliers final: 10
  residues processed: 172
  average time/residue: 0.6650
  time to fit residues: 122.8516
Evaluate side-chains
  170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  313 PHE
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain C residue  313 PHE
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  313 PHE
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 130 optimal weight:    9.9990
   chunk 61 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
B 383 GLN
C 383 GLN
D 383 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.155437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.111695 restraints weight = 12216.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.60
r_work: 0.3019 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12236  Z= 0.215
  Angle     :  0.505   5.563  16596  Z= 0.274
  Chirality :  0.039   0.130   1988
  Planarity :  0.004   0.024   2032
  Dihedral  :  3.705  13.129   1656
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.59 %
    Favored  : 80.28 %
  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:  2.80 (0.20), residues: 1504
  helix:  2.36 (0.13), residues: 1260
  sheet:  1.29 (0.68), residues: 48
  loop : -1.59 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 129 
 TYR   0.013   0.002   TYR B 175 
 PHE   0.012   0.002   PHE C 422 
 TRP   0.007   0.002   TRP A 174 
 HIS   0.003   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (12236)
  covalent geometry    : angle       0.50477 (16596)
  hydrogen bonds       : bond        0.04908 ( 1068)
  hydrogen bonds       : angle       4.22058 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.8093 (p) cc_final: 0.7867 (m)
REVERT: A   33 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7776 (mt-10)
REVERT: A   71 MET cc_start: 0.6969 (mmm) cc_final: 0.6326 (mmm)
REVERT: A  114 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7135 (mtmt)
REVERT: A  126 ARG cc_start: 0.7179 (mtm110) cc_final: 0.6409 (mtm110)
REVERT: A  131 ARG cc_start: 0.7668 (mpt-90) cc_final: 0.6104 (ttt180)
REVERT: A  155 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6156 (mtp)
REVERT: A  272 LYS cc_start: 0.7268 (tppp) cc_final: 0.6692 (ttpp)
REVERT: A  279 GLU cc_start: 0.8493 (tt0) cc_final: 0.8188 (tt0)
REVERT: A  313 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6412 (m-10)
REVERT: A  380 LYS cc_start: 0.7369 (mmtp) cc_final: 0.6917 (mmmt)
REVERT: A  399 ARG cc_start: 0.8500 (mtm180) cc_final: 0.7555 (tpt170)
REVERT: B   25 VAL cc_start: 0.8082 (p) cc_final: 0.7854 (m)
REVERT: B   33 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7758 (mt-10)
REVERT: B   71 MET cc_start: 0.6947 (mmm) cc_final: 0.6308 (mmm)
REVERT: B  114 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7154 (mtmt)
REVERT: B  126 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6418 (mtm110)
REVERT: B  131 ARG cc_start: 0.7655 (mpt-90) cc_final: 0.6117 (ttt180)
REVERT: B  155 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6233 (mtp)
REVERT: B  272 LYS cc_start: 0.7271 (tppp) cc_final: 0.6692 (ttpp)
REVERT: B  279 GLU cc_start: 0.8479 (tt0) cc_final: 0.8172 (tt0)
REVERT: B  313 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6448 (m-10)
REVERT: B  380 LYS cc_start: 0.7362 (mmtp) cc_final: 0.6910 (mmmt)
REVERT: B  399 ARG cc_start: 0.8499 (mtm180) cc_final: 0.7551 (tpt170)
REVERT: C   25 VAL cc_start: 0.8091 (p) cc_final: 0.7866 (m)
REVERT: C   33 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7779 (mt-10)
REVERT: C   71 MET cc_start: 0.6974 (mmm) cc_final: 0.6317 (mmm)
REVERT: C  114 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7144 (mtmt)
REVERT: C  126 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6395 (mtm110)
REVERT: C  131 ARG cc_start: 0.7653 (mpt-90) cc_final: 0.6111 (ttt180)
REVERT: C  155 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6170 (mtp)
REVERT: C  272 LYS cc_start: 0.7288 (tppp) cc_final: 0.6712 (ttpp)
REVERT: C  279 GLU cc_start: 0.8497 (tt0) cc_final: 0.8192 (tt0)
REVERT: C  313 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6425 (m-10)
REVERT: C  380 LYS cc_start: 0.7381 (mmtp) cc_final: 0.6931 (mmmt)
REVERT: C  399 ARG cc_start: 0.8514 (mtm180) cc_final: 0.7569 (tpt170)
REVERT: D   25 VAL cc_start: 0.8093 (p) cc_final: 0.7869 (m)
REVERT: D   33 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: D   71 MET cc_start: 0.6976 (mmm) cc_final: 0.6334 (mmm)
REVERT: D  114 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7166 (mtmt)
REVERT: D  126 ARG cc_start: 0.7148 (mtm110) cc_final: 0.6392 (mtm110)
REVERT: D  131 ARG cc_start: 0.7659 (mpt-90) cc_final: 0.6119 (ttt180)
REVERT: D  155 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6229 (mtp)
REVERT: D  272 LYS cc_start: 0.7285 (tppp) cc_final: 0.6708 (ttpp)
REVERT: D  313 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6416 (m-10)
REVERT: D  380 LYS cc_start: 0.7364 (mmtp) cc_final: 0.6920 (mmmt)
REVERT: D  399 ARG cc_start: 0.8501 (mtm180) cc_final: 0.7555 (tpt170)
  outliers start: 41
  outliers final: 13
  residues processed: 173
  average time/residue: 0.7258
  time to fit residues: 134.3145
Evaluate side-chains
  162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  313 PHE
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain C residue  155 MET
Chi-restraints excluded: chain C residue  313 PHE
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  313 PHE
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 123 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 171 ASN
A 383 GLN
B 383 GLN
C 383 GLN
D 171 ASN
D 383 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.156100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.112408 restraints weight = 12230.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.59
r_work: 0.2980 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12236  Z= 0.186
  Angle     :  0.471   5.477  16596  Z= 0.257
  Chirality :  0.037   0.130   1988
  Planarity :  0.003   0.025   2032
  Dihedral  :  3.645  13.366   1656
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.28 %
    Favored  : 80.43 %
  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:  2.87 (0.20), residues: 1504
  helix:  2.42 (0.13), residues: 1264
  sheet:  0.78 (0.65), residues: 48
  loop : -1.56 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 424 
 TYR   0.010   0.001   TYR A 175 
 PHE   0.012   0.002   PHE A  11 
 TRP   0.006   0.001   TRP B 154 
 HIS   0.002   0.001   HIS C 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (12236)
  covalent geometry    : angle       0.47113 (16596)
  hydrogen bonds       : bond        0.04682 ( 1068)
  hydrogen bonds       : angle       4.12566 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 156
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7896 (m)
REVERT: A   33 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7866 (mt-10)
REVERT: A   51 MET cc_start: 0.8560 (tpp) cc_final: 0.8340 (mmt)
REVERT: A   71 MET cc_start: 0.7100 (mmm) cc_final: 0.6514 (mmm)
REVERT: A  114 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7362 (mtmt)
REVERT: A  126 ARG cc_start: 0.7369 (mtm110) cc_final: 0.6642 (mtm110)
REVERT: A  131 ARG cc_start: 0.7847 (mpt-90) cc_final: 0.6328 (tmt-80)
REVERT: A  173 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.5801 (m-70)
REVERT: A  272 LYS cc_start: 0.7386 (tppp) cc_final: 0.6866 (ttpp)
REVERT: A  279 GLU cc_start: 0.8548 (tt0) cc_final: 0.8262 (tt0)
REVERT: A  313 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6551 (m-10)
REVERT: A  380 LYS cc_start: 0.7499 (mmtp) cc_final: 0.7061 (mmmt)
REVERT: A  399 ARG cc_start: 0.8583 (mtm180) cc_final: 0.7710 (tpt170)
REVERT: A  410 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8834 (m)
REVERT: B   25 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7890 (m)
REVERT: B   33 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: B   51 MET cc_start: 0.8570 (tpp) cc_final: 0.8353 (mmt)
REVERT: B   71 MET cc_start: 0.7081 (mmm) cc_final: 0.6497 (mmm)
REVERT: B  114 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7353 (mtmt)
REVERT: B  126 ARG cc_start: 0.7340 (mtm110) cc_final: 0.6614 (mtm110)
REVERT: B  131 ARG cc_start: 0.7842 (mpt-90) cc_final: 0.6358 (ttt180)
REVERT: B  173 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.5755 (m-70)
REVERT: B  272 LYS cc_start: 0.7384 (tppp) cc_final: 0.6864 (ttpp)
REVERT: B  279 GLU cc_start: 0.8536 (tt0) cc_final: 0.8249 (tt0)
REVERT: B  313 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6566 (m-10)
REVERT: B  331 MET cc_start: 0.7236 (ttp) cc_final: 0.6987 (ttp)
REVERT: B  380 LYS cc_start: 0.7504 (mmtp) cc_final: 0.7065 (mmmt)
REVERT: B  399 ARG cc_start: 0.8613 (mtm180) cc_final: 0.7731 (tpt170)
REVERT: C   25 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7897 (m)
REVERT: C   33 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7864 (mt-10)
REVERT: C   51 MET cc_start: 0.8565 (tpp) cc_final: 0.8347 (mmt)
REVERT: C   71 MET cc_start: 0.7116 (mmm) cc_final: 0.6487 (mmm)
REVERT: C  114 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7357 (mtmt)
REVERT: C  126 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6592 (mtm110)
REVERT: C  131 ARG cc_start: 0.7846 (mpt-90) cc_final: 0.6356 (ttt180)
REVERT: C  173 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.5755 (m-70)
REVERT: C  272 LYS cc_start: 0.7381 (tppp) cc_final: 0.6867 (ttpp)
REVERT: C  279 GLU cc_start: 0.8541 (tt0) cc_final: 0.8250 (tt0)
REVERT: C  313 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6558 (m-10)
REVERT: C  380 LYS cc_start: 0.7498 (mmtp) cc_final: 0.7062 (mmmt)
REVERT: C  399 ARG cc_start: 0.8614 (mtm180) cc_final: 0.7737 (tpt170)
REVERT: D   25 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7902 (m)
REVERT: D   33 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: D   51 MET cc_start: 0.8562 (tpp) cc_final: 0.8344 (mmt)
REVERT: D   71 MET cc_start: 0.7096 (mmm) cc_final: 0.6509 (mmm)
REVERT: D  114 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7355 (mtmt)
REVERT: D  126 ARG cc_start: 0.7312 (mtm110) cc_final: 0.6590 (mtm110)
REVERT: D  131 ARG cc_start: 0.7849 (mpt-90) cc_final: 0.6360 (ttt180)
REVERT: D  173 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5792 (m-70)
REVERT: D  272 LYS cc_start: 0.7381 (tppp) cc_final: 0.6864 (ttpp)
REVERT: D  313 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6553 (m-10)
REVERT: D  380 LYS cc_start: 0.7497 (mmtp) cc_final: 0.7066 (mmmt)
REVERT: D  399 ARG cc_start: 0.8618 (mtm180) cc_final: 0.7734 (tpt170)
  outliers start: 43
  outliers final: 11
  residues processed: 179
  average time/residue: 0.6822
  time to fit residues: 131.4089
Evaluate side-chains
  180 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  313 PHE
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  313 PHE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue   25 VAL
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain C residue  173 HIS
Chi-restraints excluded: chain C residue  313 PHE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain D residue  313 PHE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
B 383 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.158311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.115909 restraints weight = 12167.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.52
r_work: 0.3031 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12236  Z= 0.125
  Angle     :  0.409   4.984  16596  Z= 0.226
  Chirality :  0.035   0.131   1988
  Planarity :  0.003   0.026   2032
  Dihedral  :  3.494  13.699   1656
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.74 %
    Favored  : 79.82 %
  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:  3.30 (0.21), residues: 1504
  helix:  2.72 (0.13), residues: 1264
  sheet:  0.72 (0.63), residues: 48
  loop : -1.36 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 424 
 TYR   0.006   0.001   TYR B  43 
 PHE   0.010   0.001   PHE C  11 
 TRP   0.007   0.001   TRP A 154 
 HIS   0.001   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (12236)
  covalent geometry    : angle       0.40880 (16596)
  hydrogen bonds       : bond        0.04177 ( 1068)
  hydrogen bonds       : angle       3.93616 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: A   51 MET cc_start: 0.8530 (tpp) cc_final: 0.8286 (mmt)
REVERT: A   71 MET cc_start: 0.6993 (mmm) cc_final: 0.6374 (mmm)
REVERT: A  126 ARG cc_start: 0.7185 (mtm110) cc_final: 0.6437 (mtm110)
REVERT: A  131 ARG cc_start: 0.7760 (mpt-90) cc_final: 0.6204 (tmt-80)
REVERT: A  173 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.5658 (m-70)
REVERT: A  272 LYS cc_start: 0.7269 (tppp) cc_final: 0.6774 (ttpp)
REVERT: A  279 GLU cc_start: 0.8443 (tt0) cc_final: 0.8155 (tt0)
REVERT: A  331 MET cc_start: 0.7059 (ttp) cc_final: 0.6803 (ttp)
REVERT: A  380 LYS cc_start: 0.7379 (mmtp) cc_final: 0.6934 (mmmt)
REVERT: A  399 ARG cc_start: 0.8435 (mtm180) cc_final: 0.7581 (tpt170)
REVERT: A  410 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8756 (m)
REVERT: B   33 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7775 (mt-10)
REVERT: B   51 MET cc_start: 0.8533 (tpp) cc_final: 0.8287 (mmt)
REVERT: B   71 MET cc_start: 0.6966 (mmm) cc_final: 0.6351 (mmm)
REVERT: B  126 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6411 (mtm110)
REVERT: B  131 ARG cc_start: 0.7755 (mpt-90) cc_final: 0.6242 (ttt180)
REVERT: B  173 HIS cc_start: 0.6568 (OUTLIER) cc_final: 0.5632 (m-70)
REVERT: B  272 LYS cc_start: 0.7270 (tppp) cc_final: 0.6775 (ttpp)
REVERT: B  279 GLU cc_start: 0.8431 (tt0) cc_final: 0.8143 (tt0)
REVERT: B  331 MET cc_start: 0.7069 (ttp) cc_final: 0.6812 (ttp)
REVERT: B  380 LYS cc_start: 0.7381 (mmtp) cc_final: 0.6934 (mmmt)
REVERT: B  399 ARG cc_start: 0.8463 (mtm180) cc_final: 0.7601 (tpt170)
REVERT: B  410 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8758 (m)
REVERT: C   33 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7796 (mt-10)
REVERT: C   51 MET cc_start: 0.8535 (tpp) cc_final: 0.8291 (mmt)
REVERT: C   71 MET cc_start: 0.6932 (mmm) cc_final: 0.6282 (mmm)
REVERT: C  114 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7180 (mtmt)
REVERT: C  126 ARG cc_start: 0.7146 (mtm110) cc_final: 0.6405 (mtm110)
REVERT: C  131 ARG cc_start: 0.7749 (mpt-90) cc_final: 0.6205 (tmt-80)
REVERT: C  173 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.5661 (m-70)
REVERT: C  272 LYS cc_start: 0.7281 (tppp) cc_final: 0.6787 (ttpp)
REVERT: C  279 GLU cc_start: 0.8440 (tt0) cc_final: 0.8148 (tt0)
REVERT: C  331 MET cc_start: 0.7079 (ttp) cc_final: 0.6823 (ttp)
REVERT: C  380 LYS cc_start: 0.7375 (mmtp) cc_final: 0.6932 (mmmt)
REVERT: C  399 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7605 (tpt170)
REVERT: C  410 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8754 (m)
REVERT: D   33 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7796 (mt-10)
REVERT: D   51 MET cc_start: 0.8537 (tpp) cc_final: 0.8291 (mmt)
REVERT: D   71 MET cc_start: 0.6978 (mmm) cc_final: 0.6361 (mmm)
REVERT: D  114 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7185 (mtmt)
REVERT: D  126 ARG cc_start: 0.7148 (mtm110) cc_final: 0.6404 (mtm110)
REVERT: D  131 ARG cc_start: 0.7754 (mpt-90) cc_final: 0.6237 (ttt180)
REVERT: D  173 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5599 (m-70)
REVERT: D  272 LYS cc_start: 0.7292 (tppp) cc_final: 0.6780 (ttpp)
REVERT: D  331 MET cc_start: 0.7083 (ttp) cc_final: 0.6825 (ttp)
REVERT: D  380 LYS cc_start: 0.7388 (mmtp) cc_final: 0.6950 (mmmt)
REVERT: D  399 ARG cc_start: 0.8445 (mtm180) cc_final: 0.7602 (tpt170)
REVERT: D  410 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8756 (m)
  outliers start: 32
  outliers final: 8
  residues processed: 184
  average time/residue: 0.5534
  time to fit residues: 110.4134
Evaluate side-chains
  176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain C residue  173 HIS
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  404 ILE
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   chunk 139 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 145 optimal weight:    1.9990
   chunk 102 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 132 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
B 171 ASN
B 383 GLN
C 171 ASN
C 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.158018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.115334 restraints weight = 12070.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.53
r_work: 0.3021 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12236  Z= 0.136
  Angle     :  0.420   5.032  16596  Z= 0.232
  Chirality :  0.035   0.132   1988
  Planarity :  0.003   0.026   2032
  Dihedral  :  3.479  13.378   1656
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 19.80 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.34 (0.21), residues: 1504
  helix:  2.75 (0.13), residues: 1264
  sheet:  0.56 (0.62), residues: 48
  loop : -1.38 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 129 
 TYR   0.008   0.001   TYR D 175 
 PHE   0.012   0.002   PHE A 422 
 TRP   0.006   0.001   TRP B 154 
 HIS   0.001   0.000   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12236)
  covalent geometry    : angle       0.42050 (16596)
  hydrogen bonds       : bond        0.04256 ( 1068)
  hydrogen bonds       : angle       3.92100 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7852 (mt-10)
REVERT: A   51 MET cc_start: 0.8539 (tpp) cc_final: 0.8276 (mmt)
REVERT: A   71 MET cc_start: 0.7013 (mmm) cc_final: 0.6395 (mmm)
REVERT: A  114 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7262 (mtmt)
REVERT: A  126 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6468 (mtm110)
REVERT: A  131 ARG cc_start: 0.7791 (mpt-90) cc_final: 0.6284 (ttt180)
REVERT: A  173 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.5607 (m-70)
REVERT: A  272 LYS cc_start: 0.7338 (tppp) cc_final: 0.6841 (ttpp)
REVERT: A  279 GLU cc_start: 0.8463 (tt0) cc_final: 0.8128 (tt0)
REVERT: A  283 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8688 (mttt)
REVERT: A  331 MET cc_start: 0.7135 (ttp) cc_final: 0.6877 (ttp)
REVERT: A  364 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7174 (mm-30)
REVERT: A  380 LYS cc_start: 0.7440 (mmtp) cc_final: 0.6997 (mmmt)
REVERT: A  399 ARG cc_start: 0.8489 (mtm180) cc_final: 0.7677 (tpt170)
REVERT: A  410 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8785 (m)
REVERT: B   33 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: B   51 MET cc_start: 0.8546 (tpp) cc_final: 0.8283 (mmt)
REVERT: B   71 MET cc_start: 0.7005 (mmm) cc_final: 0.6392 (mmm)
REVERT: B  114 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7269 (mtmt)
REVERT: B  126 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6475 (mtm110)
REVERT: B  131 ARG cc_start: 0.7870 (tpt-90) cc_final: 0.6330 (ttt180)
REVERT: B  173 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.5535 (m-70)
REVERT: B  272 LYS cc_start: 0.7338 (tppp) cc_final: 0.6843 (ttpp)
REVERT: B  279 GLU cc_start: 0.8455 (tt0) cc_final: 0.8123 (tt0)
REVERT: B  283 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8695 (mttt)
REVERT: B  331 MET cc_start: 0.7147 (ttp) cc_final: 0.6887 (ttp)
REVERT: B  364 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7128 (mm-30)
REVERT: B  380 LYS cc_start: 0.7445 (mmtp) cc_final: 0.7001 (mmmt)
REVERT: B  399 ARG cc_start: 0.8497 (mtm180) cc_final: 0.7666 (tpt170)
REVERT: B  410 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8788 (m)
REVERT: C   33 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7860 (mt-10)
REVERT: C   51 MET cc_start: 0.8544 (tpp) cc_final: 0.8282 (mmt)
REVERT: C   71 MET cc_start: 0.7000 (mmm) cc_final: 0.6362 (mmm)
REVERT: C  126 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6450 (mtm110)
REVERT: C  131 ARG cc_start: 0.7775 (mpt-90) cc_final: 0.6295 (ttt180)
REVERT: C  173 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5509 (m-70)
REVERT: C  272 LYS cc_start: 0.7353 (tppp) cc_final: 0.6854 (ttpp)
REVERT: C  279 GLU cc_start: 0.8462 (tt0) cc_final: 0.8124 (tt0)
REVERT: C  331 MET cc_start: 0.7155 (ttp) cc_final: 0.6894 (ttp)
REVERT: C  364 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7124 (mm-30)
REVERT: C  380 LYS cc_start: 0.7439 (mmtp) cc_final: 0.6998 (mmmt)
REVERT: C  399 ARG cc_start: 0.8486 (mtm180) cc_final: 0.7662 (tpt170)
REVERT: C  410 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8785 (m)
REVERT: D   33 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7869 (mt-10)
REVERT: D   51 MET cc_start: 0.8541 (tpp) cc_final: 0.8276 (mmt)
REVERT: D   71 MET cc_start: 0.7018 (mmm) cc_final: 0.6397 (mmm)
REVERT: D  126 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6459 (mtm110)
REVERT: D  131 ARG cc_start: 0.7870 (tpt-90) cc_final: 0.6323 (ttt180)
REVERT: D  173 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5561 (m-70)
REVERT: D  272 LYS cc_start: 0.7346 (tppp) cc_final: 0.6850 (ttpp)
REVERT: D  331 MET cc_start: 0.7159 (ttp) cc_final: 0.6899 (ttp)
REVERT: D  364 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7164 (mm-30)
REVERT: D  380 LYS cc_start: 0.7444 (mmtp) cc_final: 0.7001 (mmmt)
REVERT: D  399 ARG cc_start: 0.8486 (mtm180) cc_final: 0.7662 (tpt170)
REVERT: D  410 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8784 (m)
  outliers start: 27
  outliers final: 8
  residues processed: 177
  average time/residue: 0.5694
  time to fit residues: 108.7599
Evaluate side-chains
  176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue  173 HIS
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  404 ILE
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 144 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 99 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 137 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.159199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.115906 restraints weight = 12073.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.59
r_work: 0.3031 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12236  Z= 0.118
  Angle     :  0.400   4.954  16596  Z= 0.222
  Chirality :  0.034   0.132   1988
  Planarity :  0.003   0.026   2032
  Dihedral  :  3.402  13.069   1656
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.18 %
    Favored  : 77.91 %
  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:  3.50 (0.21), residues: 1504
  helix:  2.88 (0.13), residues: 1264
  sheet:  0.21 (0.52), residues: 48
  loop : -1.37 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.006   0.001   TYR C 175 
 PHE   0.009   0.001   PHE A  11 
 TRP   0.007   0.001   TRP B 154 
 HIS   0.001   0.000   HIS D 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (12236)
  covalent geometry    : angle       0.39972 (16596)
  hydrogen bonds       : bond        0.04045 ( 1068)
  hydrogen bonds       : angle       3.82645 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7888 (mt-10)
REVERT: A   51 MET cc_start: 0.8564 (tpp) cc_final: 0.8316 (mmt)
REVERT: A  114 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7285 (mtmt)
REVERT: A  126 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6490 (mtm110)
REVERT: A  131 ARG cc_start: 0.7902 (mpt-90) cc_final: 0.6370 (ttt180)
REVERT: A  173 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.5613 (m-70)
REVERT: A  272 LYS cc_start: 0.7369 (tppp) cc_final: 0.6905 (ttpp)
REVERT: A  279 GLU cc_start: 0.8462 (tt0) cc_final: 0.8128 (tt0)
REVERT: A  331 MET cc_start: 0.7184 (ttp) cc_final: 0.6925 (ttp)
REVERT: A  364 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7248 (mm-30)
REVERT: A  380 LYS cc_start: 0.7452 (mmtp) cc_final: 0.7027 (mmmt)
REVERT: A  399 ARG cc_start: 0.8487 (mtm180) cc_final: 0.7667 (tpt170)
REVERT: A  410 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8795 (m)
REVERT: B   51 MET cc_start: 0.8595 (tpp) cc_final: 0.8353 (mmt)
REVERT: B  114 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7278 (mtmt)
REVERT: B  126 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6546 (mtm110)
REVERT: B  131 ARG cc_start: 0.7863 (tpt-90) cc_final: 0.6345 (ttt180)
REVERT: B  173 HIS cc_start: 0.6560 (OUTLIER) cc_final: 0.5587 (m-70)
REVERT: B  272 LYS cc_start: 0.7368 (tppp) cc_final: 0.6905 (ttpp)
REVERT: B  279 GLU cc_start: 0.8459 (tt0) cc_final: 0.8126 (tt0)
REVERT: B  331 MET cc_start: 0.7189 (ttp) cc_final: 0.6930 (ttp)
REVERT: B  364 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7197 (mm-30)
REVERT: B  380 LYS cc_start: 0.7438 (mmtp) cc_final: 0.7021 (mmmt)
REVERT: B  399 ARG cc_start: 0.8497 (mtm180) cc_final: 0.7678 (tpt170)
REVERT: B  410 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8827 (m)
REVERT: C   33 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7876 (mt-10)
REVERT: C   51 MET cc_start: 0.8564 (tpp) cc_final: 0.8326 (mmt)
REVERT: C  114 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7297 (mtmt)
REVERT: C  126 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6465 (mtm110)
REVERT: C  131 ARG cc_start: 0.7863 (tpt-90) cc_final: 0.6350 (ttt180)
REVERT: C  173 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.5605 (m-70)
REVERT: C  272 LYS cc_start: 0.7443 (tppp) cc_final: 0.6983 (ttpp)
REVERT: C  279 GLU cc_start: 0.8466 (tt0) cc_final: 0.8129 (tt0)
REVERT: C  283 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8679 (mttt)
REVERT: C  331 MET cc_start: 0.7200 (ttp) cc_final: 0.6940 (ttp)
REVERT: C  364 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7190 (mm-30)
REVERT: C  380 LYS cc_start: 0.7440 (mmtp) cc_final: 0.7029 (mmmt)
REVERT: C  399 ARG cc_start: 0.8488 (mtm180) cc_final: 0.7674 (tpt170)
REVERT: C  410 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8823 (m)
REVERT: D   33 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: D   51 MET cc_start: 0.8540 (tpp) cc_final: 0.8298 (mmt)
REVERT: D  114 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7292 (mtmt)
REVERT: D  126 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6529 (mtm110)
REVERT: D  131 ARG cc_start: 0.7861 (tpt-90) cc_final: 0.6331 (ttt180)
REVERT: D  173 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.5531 (m-70)
REVERT: D  272 LYS cc_start: 0.7428 (tppp) cc_final: 0.6989 (ttpp)
REVERT: D  331 MET cc_start: 0.7209 (ttp) cc_final: 0.6951 (ttp)
REVERT: D  364 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7142 (mm-30)
REVERT: D  380 LYS cc_start: 0.7437 (mmtp) cc_final: 0.7021 (mmmt)
REVERT: D  399 ARG cc_start: 0.8484 (mtm180) cc_final: 0.7670 (tpt170)
REVERT: D  410 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8821 (m)
  outliers start: 25
  outliers final: 8
  residues processed: 182
  average time/residue: 0.5744
  time to fit residues: 112.4319
Evaluate side-chains
  181 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain C residue  173 HIS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  404 ILE
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 117 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 383 GLN
B 189 GLN
B 383 GLN
C 189 GLN
C 383 GLN
D 189 GLN
D 383 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.157529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.114125 restraints weight = 11991.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.58
r_work: 0.3002 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12236  Z= 0.150
  Angle     :  0.429   5.091  16596  Z= 0.236
  Chirality :  0.036   0.132   1988
  Planarity :  0.003   0.025   2032
  Dihedral  :  3.493  13.195   1656
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.11 %
    Favored  : 77.52 %
  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:  3.33 (0.21), residues: 1504
  helix:  2.77 (0.13), residues: 1264
  sheet:  0.08 (0.51), residues: 48
  loop : -1.43 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.008   0.001   TYR C 175 
 PHE   0.010   0.002   PHE C 422 
 TRP   0.006   0.001   TRP A 154 
 HIS   0.002   0.001   HIS D 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12236)
  covalent geometry    : angle       0.42931 (16596)
  hydrogen bonds       : bond        0.04324 ( 1068)
  hydrogen bonds       : angle       3.90604 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7554 (tt0)
REVERT: A   51 MET cc_start: 0.8590 (tpp) cc_final: 0.8387 (mmt)
REVERT: A  114 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7345 (mtmt)
REVERT: A  126 ARG cc_start: 0.7290 (mtm110) cc_final: 0.6497 (mtm110)
REVERT: A  131 ARG cc_start: 0.7910 (mpt-90) cc_final: 0.6390 (ttt180)
REVERT: A  173 HIS cc_start: 0.6519 (OUTLIER) cc_final: 0.5506 (m-70)
REVERT: A  272 LYS cc_start: 0.7395 (tppp) cc_final: 0.6924 (ttpp)
REVERT: A  279 GLU cc_start: 0.8496 (tt0) cc_final: 0.8165 (tt0)
REVERT: A  283 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8738 (mttt)
REVERT: A  331 MET cc_start: 0.7279 (ttp) cc_final: 0.7032 (ttp)
REVERT: A  364 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7218 (mm-30)
REVERT: A  380 LYS cc_start: 0.7499 (mmtp) cc_final: 0.7058 (mmmt)
REVERT: A  399 ARG cc_start: 0.8520 (mtm180) cc_final: 0.7711 (tpt170)
REVERT: A  410 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.8807 (m)
REVERT: B   51 MET cc_start: 0.8595 (tpp) cc_final: 0.8393 (mmt)
REVERT: B   71 MET cc_start: 0.7021 (mmm) cc_final: 0.6420 (mmm)
REVERT: B  114 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7349 (mtmt)
REVERT: B  126 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6528 (mtm110)
REVERT: B  131 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.6392 (ttt180)
REVERT: B  173 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.5479 (m-70)
REVERT: B  272 LYS cc_start: 0.7390 (tppp) cc_final: 0.6917 (ttpp)
REVERT: B  279 GLU cc_start: 0.8487 (tt0) cc_final: 0.8159 (tt0)
REVERT: B  283 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8740 (mttt)
REVERT: B  331 MET cc_start: 0.7294 (ttp) cc_final: 0.7044 (ttp)
REVERT: B  364 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7167 (mm-30)
REVERT: B  380 LYS cc_start: 0.7462 (mmtp) cc_final: 0.7023 (mmmt)
REVERT: B  399 ARG cc_start: 0.8525 (mtm180) cc_final: 0.7716 (tpt170)
REVERT: B  410 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.8807 (m)
REVERT: C   33 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7539 (tt0)
REVERT: C   51 MET cc_start: 0.8591 (tpp) cc_final: 0.8390 (mmt)
REVERT: C  114 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7344 (mtmt)
REVERT: C  126 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6502 (mtm110)
REVERT: C  131 ARG cc_start: 0.7916 (tpt-90) cc_final: 0.6386 (ttt180)
REVERT: C  173 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.5507 (m-70)
REVERT: C  272 LYS cc_start: 0.7382 (tppp) cc_final: 0.6928 (ttpp)
REVERT: C  279 GLU cc_start: 0.8491 (tt0) cc_final: 0.8164 (tt0)
REVERT: C  283 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8741 (mttt)
REVERT: C  331 MET cc_start: 0.7306 (ttp) cc_final: 0.7056 (ttp)
REVERT: C  364 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7160 (mm-30)
REVERT: C  380 LYS cc_start: 0.7457 (mmtp) cc_final: 0.7022 (mmmt)
REVERT: C  399 ARG cc_start: 0.8528 (mtm180) cc_final: 0.7714 (tpt170)
REVERT: C  410 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8806 (m)
REVERT: D   33 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7542 (tt0)
REVERT: D   51 MET cc_start: 0.8594 (tpp) cc_final: 0.8393 (mmt)
REVERT: D  114 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7337 (mtmt)
REVERT: D  126 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6520 (mtm110)
REVERT: D  131 ARG cc_start: 0.7917 (tpt-90) cc_final: 0.6386 (ttt180)
REVERT: D  173 HIS cc_start: 0.6539 (OUTLIER) cc_final: 0.5568 (m-70)
REVERT: D  272 LYS cc_start: 0.7379 (tppp) cc_final: 0.6929 (ttpp)
REVERT: D  331 MET cc_start: 0.7307 (ttp) cc_final: 0.7056 (ttp)
REVERT: D  364 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7157 (mm-30)
REVERT: D  380 LYS cc_start: 0.7445 (mmtp) cc_final: 0.7009 (mmmt)
REVERT: D  399 ARG cc_start: 0.8523 (mtm180) cc_final: 0.7715 (tpt170)
REVERT: D  410 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8807 (m)
  outliers start: 31
  outliers final: 12
  residues processed: 171
  average time/residue: 0.6003
  time to fit residues: 110.4109
Evaluate side-chains
  175 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain C residue  173 HIS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  404 ILE
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 147 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0370
   chunk 124 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 133 optimal weight:    4.9990
   chunk 139 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.159955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.117653 restraints weight = 12150.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.52
r_work: 0.3099 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12236  Z= 0.111
  Angle     :  0.395   4.853  16596  Z= 0.219
  Chirality :  0.034   0.132   1988
  Planarity :  0.003   0.026   2032
  Dihedral  :  3.388  13.113   1656
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.41 %
    Favored  : 77.52 %
  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:  3.58 (0.21), residues: 1504
  helix:  2.94 (0.13), residues: 1264
  sheet:  0.07 (0.47), residues: 48
  loop : -1.30 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  26 
 TYR   0.006   0.001   TYR B  96 
 PHE   0.009   0.001   PHE B  11 
 TRP   0.008   0.001   TRP B 154 
 HIS   0.001   0.000   HIS D 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (12236)
  covalent geometry    : angle       0.39520 (16596)
  hydrogen bonds       : bond        0.03979 ( 1068)
  hydrogen bonds       : angle       3.78679 ( 3204)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7377 (tt0)
REVERT: A   51 MET cc_start: 0.8368 (tpp) cc_final: 0.8120 (mmt)
REVERT: A  114 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7039 (mtmt)
REVERT: A  126 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6259 (mtm110)
REVERT: A  131 ARG cc_start: 0.7677 (mpt-90) cc_final: 0.6049 (ttt180)
REVERT: A  173 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.5466 (m-70)
REVERT: A  272 LYS cc_start: 0.7216 (tppp) cc_final: 0.6711 (ttpp)
REVERT: A  279 GLU cc_start: 0.8354 (tt0) cc_final: 0.7972 (tt0)
REVERT: A  283 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8506 (mttt)
REVERT: A  331 MET cc_start: 0.6904 (ttp) cc_final: 0.6645 (ttp)
REVERT: A  364 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7029 (mm-30)
REVERT: A  380 LYS cc_start: 0.7251 (mmtp) cc_final: 0.6803 (mmmt)
REVERT: A  399 ARG cc_start: 0.8313 (mtm180) cc_final: 0.7481 (tpt170)
REVERT: A  410 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8637 (m)
REVERT: B   51 MET cc_start: 0.8361 (tpp) cc_final: 0.8111 (mmt)
REVERT: B  114 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7039 (mtmt)
REVERT: B  126 ARG cc_start: 0.7084 (mtm110) cc_final: 0.6246 (mtm110)
REVERT: B  131 ARG cc_start: 0.7695 (tpt-90) cc_final: 0.6068 (ttt180)
REVERT: B  173 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5451 (m-70)
REVERT: B  272 LYS cc_start: 0.7215 (tppp) cc_final: 0.6706 (ttpp)
REVERT: B  279 GLU cc_start: 0.8362 (tt0) cc_final: 0.7982 (tt0)
REVERT: B  283 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8515 (mttt)
REVERT: B  331 MET cc_start: 0.6897 (ttp) cc_final: 0.6638 (ttp)
REVERT: B  364 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6934 (mm-30)
REVERT: B  380 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6815 (mmmt)
REVERT: B  399 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7503 (tpt170)
REVERT: B  410 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8671 (m)
REVERT: C   33 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7371 (tt0)
REVERT: C   51 MET cc_start: 0.8365 (tpp) cc_final: 0.8116 (mmt)
REVERT: C  126 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6216 (mtm110)
REVERT: C  131 ARG cc_start: 0.7690 (tpt-90) cc_final: 0.6064 (ttt180)
REVERT: C  173 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.5473 (m-70)
REVERT: C  272 LYS cc_start: 0.7230 (tppp) cc_final: 0.6720 (ttpp)
REVERT: C  279 GLU cc_start: 0.8357 (tt0) cc_final: 0.7980 (tt0)
REVERT: C  283 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8493 (mttt)
REVERT: C  331 MET cc_start: 0.6912 (ttp) cc_final: 0.6652 (ttp)
REVERT: C  364 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6941 (mm-30)
REVERT: C  380 LYS cc_start: 0.7258 (mmtp) cc_final: 0.6815 (mmmt)
REVERT: C  399 ARG cc_start: 0.8328 (mtm180) cc_final: 0.7491 (tpt170)
REVERT: C  410 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8645 (m)
REVERT: D   33 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7727 (mt-10)
REVERT: D   51 MET cc_start: 0.8355 (tpp) cc_final: 0.8107 (mmt)
REVERT: D  114 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7067 (mtmt)
REVERT: D  126 ARG cc_start: 0.7056 (mtm110) cc_final: 0.6215 (mtm110)
REVERT: D  131 ARG cc_start: 0.7656 (tpt-90) cc_final: 0.6030 (ttt180)
REVERT: D  173 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5457 (m-70)
REVERT: D  272 LYS cc_start: 0.7282 (tppp) cc_final: 0.6803 (ttpp)
REVERT: D  331 MET cc_start: 0.6921 (ttp) cc_final: 0.6663 (ttp)
REVERT: D  364 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6937 (mm-30)
REVERT: D  380 LYS cc_start: 0.7260 (mmtp) cc_final: 0.6821 (mmmt)
REVERT: D  399 ARG cc_start: 0.8327 (mtm180) cc_final: 0.7503 (tpt170)
REVERT: D  410 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8631 (m)
  outliers start: 27
  outliers final: 10
  residues processed: 180
  average time/residue: 0.6658
  time to fit residues: 129.1102
Evaluate side-chains
  180 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  173 HIS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain D residue  404 ILE
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 146 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 150 optimal weight:    3.9990
   chunk 132 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 124 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
B 383 GLN
C 383 GLN
D 383 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.156824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.113396 restraints weight = 12063.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.59
r_work: 0.3046 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12236  Z= 0.175
  Angle     :  0.456   5.205  16596  Z= 0.250
  Chirality :  0.037   0.133   1988
  Planarity :  0.003   0.025   2032
  Dihedral  :  3.565  13.266   1656
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.18 %
    Favored  : 77.52 %
  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:  3.20 (0.20), residues: 1504
  helix:  2.69 (0.13), residues: 1264
  sheet: -0.08 (0.48), residues: 48
  loop : -1.50 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 340 
 TYR   0.009   0.001   TYR A 175 
 PHE   0.013   0.002   PHE B 422 
 TRP   0.006   0.001   TRP D 174 
 HIS   0.003   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12236)
  covalent geometry    : angle       0.45633 (16596)
  hydrogen bonds       : bond        0.04525 ( 1068)
  hydrogen bonds       : angle       3.96507 ( 3204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4218.18 seconds
wall clock time: 72 minutes 40.88 seconds (4360.88 seconds total)