Starting phenix.real_space_refine
on Mon Aug 25 01:17:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jma_36411/08_2025/8jma_36411_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jma_36411/08_2025/8jma_36411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jma_36411/08_2025/8jma_36411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jma_36411/08_2025/8jma_36411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jma_36411/08_2025/8jma_36411_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jma_36411/08_2025/8jma_36411_neut_trim.cif"
  }
  resolution = 2.5
  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: 5
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    7848      2.51       5
     N    2056      2.21       5
     O    2120      1.98       5
     H   12472      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 24568
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 6130
          Classifications: {'peptide': 381}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 374}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 6.71, per 1000 atoms: 0.27
  Number of scatterers: 24568
  At special positions: 0
  Unit cell: (110.67, 110.67, 105.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     O    2120      8.00
     N    2056      7.00
     C    7848      6.00
     H   12472      1.00
    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: 1.85
  Conformation dependent library (CDL) restraints added in 799.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2904

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      85.0% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 37 through 65
    Processing helix  chain 'A' and resid 73 through 100
      removed outlier: 3.550A  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
    Processing helix  chain 'A' and resid 124 through 161
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.509A  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: 6.068A  pdb=" N   ILE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA A 295 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 357
      Proline residue:  A 347  - end of helix
    Processing helix  chain 'A' and resid 357 through 368
      removed outlier: 3.764A  pdb=" N   ILE A 361 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL A 387 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 425
      removed outlier: 3.708A  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 65
    Processing helix  chain 'B' and resid 73 through 100
      removed outlier: 3.550A  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
    Processing helix  chain 'B' and resid 124 through 161
    Processing helix  chain 'B' and resid 168 through 174
      removed outlier: 3.509A  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: 6.068A  pdb=" N   ILE B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   ALA B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 357
      Proline residue:  B 347  - end of helix
    Processing helix  chain 'B' and resid 357 through 368
      removed outlier: 3.764A  pdb=" N   ILE B 361 " --> pdb=" O   LYS B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL B 387 " --> pdb=" O   GLN B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 425
      removed outlier: 3.710A  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 65
    Processing helix  chain 'C' and resid 73 through 100
      removed outlier: 3.550A  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
    Processing helix  chain 'C' and resid 124 through 161
    Processing helix  chain 'C' and resid 168 through 174
      removed outlier: 3.509A  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: 6.068A  pdb=" N   ILE C 294 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA C 295 " --> pdb=" O   SER C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 357
      Proline residue:  C 347  - end of helix
    Processing helix  chain 'C' and resid 357 through 368
      removed outlier: 3.763A  pdb=" N   ILE C 361 " --> pdb=" O   LYS C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL C 387 " --> pdb=" O   GLN C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 425
      removed outlier: 3.708A  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 65
    Processing helix  chain 'D' and resid 73 through 100
      removed outlier: 3.550A  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
    Processing helix  chain 'D' and resid 124 through 161
    Processing helix  chain 'D' and resid 168 through 174
      removed outlier: 3.509A  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: 6.068A  pdb=" N   ILE D 294 " --> pdb=" O   ASN D 290 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA D 295 " --> pdb=" O   SER D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 357
      Proline residue:  D 347  - end of helix
    Processing helix  chain 'D' and resid 357 through 368
      removed outlier: 3.764A  pdb=" N   ILE D 361 " --> pdb=" O   LYS D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL D 387 " --> pdb=" O   GLN D 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 402 through 425
      removed outlier: 3.708A  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
    Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393
      removed outlier: 4.635A  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
    Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393
      removed outlier: 4.635A  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
    Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393
      removed outlier: 4.635A  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
    Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393
      removed outlier: 4.635A  pdb=" N   PHE D 392 " --> pdb=" O   VAL D 400 " (cutoff:3.500A)

    1072 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: 7.26

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 12440
        1.02 -     1.21: 32
        1.21 -     1.41: 5022
        1.41 -     1.61: 7194
        1.61 -     1.81: 112
  Bond restraints: 24800
  Sorted by residual:
  bond pdb=" C2  FRU C 501 "
       pdb=" O5  FRU C 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C2  FRU B 501 "
       pdb=" O5  FRU B 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C2  FRU D 501 "
       pdb=" O5  FRU D 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C2  FRU A 501 "
       pdb=" O5  FRU A 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C5  FRU B 501 "
       pdb=" O5  FRU B 501 "
    ideal  model  delta    sigma   weight residual
    1.420  1.486 -0.066 2.00e-02 2.50e+03 1.08e+01
  ... (remaining 24795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 42733
        1.16 -     2.33: 1910
        2.33 -     3.49: 106
        3.49 -     4.65: 31
        4.65 -     5.81: 12
  Bond angle restraints: 44792
  Sorted by residual:
  angle pdb=" C   ILE A 418 "
        pdb=" CA  ILE A 418 "
        pdb=" CB  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.82    4.20 1.31e+00 5.83e-01 1.03e+01
  angle pdb=" C   ILE D 418 "
        pdb=" CA  ILE D 418 "
        pdb=" CB  ILE D 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.85    4.17 1.31e+00 5.83e-01 1.01e+01
  angle pdb=" C   ILE C 418 "
        pdb=" CA  ILE C 418 "
        pdb=" CB  ILE C 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.87    4.15 1.31e+00 5.83e-01 1.00e+01
  angle pdb=" C   ILE B 418 "
        pdb=" CA  ILE B 418 "
        pdb=" CB  ILE B 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.91    4.11 1.31e+00 5.83e-01 9.86e+00
  angle pdb=" C   VAL A 417 "
        pdb=" CA  VAL A 417 "
        pdb=" CB  VAL A 417 "
      ideal   model   delta    sigma   weight residual
     112.14  108.36    3.78 1.35e+00 5.49e-01 7.85e+00
  ... (remaining 44787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 10306
       17.25 -    34.50: 910
       34.50 -    51.75: 220
       51.75 -    69.00: 160
       69.00 -    86.25: 8
  Dihedral angle restraints: 11604
    sinusoidal: 6272
      harmonic: 5332
  Sorted by residual:
  dihedral pdb=" CB  GLU B  66 "
           pdb=" CG  GLU B  66 "
           pdb=" CD  GLU B  66 "
           pdb=" OE1 GLU B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.25  -86.25     1      3.00e+01 1.11e-03 9.97e+00
  dihedral pdb=" CB  GLU A  66 "
           pdb=" CG  GLU A  66 "
           pdb=" CD  GLU A  66 "
           pdb=" OE1 GLU A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.20  -86.20     1      3.00e+01 1.11e-03 9.96e+00
  dihedral pdb=" CB  GLU D  66 "
           pdb=" CG  GLU D  66 "
           pdb=" CD  GLU D  66 "
           pdb=" OE1 GLU D  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.20  -86.20     1      3.00e+01 1.11e-03 9.96e+00
  ... (remaining 11601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1212
       0.025 -    0.050: 474
       0.050 -    0.075: 252
       0.075 -    0.100: 50
       0.100 -    0.125: 24
  Chirality restraints: 2012
  Sorted by residual:
  chirality pdb=" CA  ILE A   3 "
            pdb=" N   ILE A   3 "
            pdb=" C   ILE A   3 "
            pdb=" CB  ILE A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE B   3 "
            pdb=" N   ILE B   3 "
            pdb=" C   ILE B   3 "
            pdb=" CB  ILE B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE D   3 "
            pdb=" N   ILE D   3 "
            pdb=" C   ILE D   3 "
            pdb=" CB  ILE D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 2009 not shown)

  Planarity restraints: 3532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 413 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ALA A 413 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 413 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 414 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 413 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ALA D 413 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA D 413 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR D 414 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 413 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ALA B 413 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA B 413 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR B 414 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 3529 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 1675
        2.21 -     2.80: 52319
        2.80 -     3.40: 73625
        3.40 -     4.00: 94551
        4.00 -     4.60: 147383
  Nonbonded interactions: 369553
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 401 "
            pdb=" HG1 THR A 403 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OD1 ASN D 401 "
            pdb=" HG1 THR D 403 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD1 ASN B 401 "
            pdb=" HG1 THR B 403 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD1 ASN C 401 "
            pdb=" HG1 THR C 403 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" H   ASN C  27 "
            pdb=" O   ARG C  31 "
     model   vdw
     1.615 2.450
  ... (remaining 369548 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: 0.04
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:                  0.010
  Normalize map: mean=0, sd=1:             1.460
  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:             0.160
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     27.830
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  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:9.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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      :  0.004   0.071  12328  Z= 0.219
  Angle     :  0.512   5.813  16728  Z= 0.282
  Chirality :  0.035   0.125   2012
  Planarity :  0.004   0.022   2040
  Dihedral  : 16.386  86.254   4472
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 17.93 %
    Favored  : 81.46 %
  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:  3.05 (0.21), residues: 1508
  helix:  2.43 (0.14), residues: 1264
  sheet:  1.30 (0.74), residues: 48
  loop : -0.65 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.007   0.001   TYR A 415 
 PHE   0.011   0.001   PHE A 298 
 TRP   0.006   0.001   TRP D 328 
 HIS   0.003   0.001   HIS C 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (12328)
  covalent geometry    : angle       0.51192 (16728)
  hydrogen bonds       : bond        0.09802 ( 1072)
  hydrogen bonds       : angle       4.78280 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7336 (mp0)
REVERT: B   33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7335 (mp0)
REVERT: C   33 GLU cc_start: 0.7562 (mp0) cc_final: 0.7333 (mp0)
REVERT: D   33 GLU cc_start: 0.7559 (mp0) cc_final: 0.7334 (mp0)
  outliers start: 8
  outliers final: 8
  residues processed: 168
  average time/residue: 1.1798
  time to fit residues: 215.3973
Evaluate side-chains
  168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.099512 restraints weight = 35773.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.67
r_work: 0.2895 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.0498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12328  Z= 0.162
  Angle     :  0.458   3.942  16728  Z= 0.253
  Chirality :  0.035   0.132   2012
  Planarity :  0.003   0.028   2040
  Dihedral  :  4.289  25.110   1764
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.41 %
    Favored  : 82.07 %
  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:  3.52 (0.21), residues: 1508
  helix:  2.77 (0.13), residues: 1264
  sheet:  0.81 (0.79), residues: 48
  loop : -0.44 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 129 
 TYR   0.010   0.001   TYR D 415 
 PHE   0.010   0.001   PHE D  11 
 TRP   0.005   0.001   TRP A 154 
 HIS   0.003   0.001   HIS C 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (12328)
  covalent geometry    : angle       0.45786 (16728)
  hydrogen bonds       : bond        0.04547 ( 1072)
  hydrogen bonds       : angle       4.12632 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7865 (mp0) cc_final: 0.7592 (mp0)
REVERT: A  420 ILE cc_start: 0.8759 (mm) cc_final: 0.8509 (mt)
REVERT: B   33 GLU cc_start: 0.7850 (mp0) cc_final: 0.7575 (mp0)
REVERT: B  420 ILE cc_start: 0.8752 (mm) cc_final: 0.8500 (mt)
REVERT: C   33 GLU cc_start: 0.7859 (mp0) cc_final: 0.7585 (mp0)
REVERT: C  420 ILE cc_start: 0.8752 (mm) cc_final: 0.8496 (mt)
REVERT: D   33 GLU cc_start: 0.7842 (mp0) cc_final: 0.7569 (mp0)
REVERT: D  420 ILE cc_start: 0.8755 (mm) cc_final: 0.8502 (mt)
  outliers start: 20
  outliers final: 12
  residues processed: 192
  average time/residue: 1.2878
  time to fit residues: 267.7292
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 147 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0570
   overall best weight:    1.5502

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.140706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101797 restraints weight = 35410.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.67
r_work: 0.2903 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.0719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12328  Z= 0.147
  Angle     :  0.449   3.776  16728  Z= 0.244
  Chirality :  0.034   0.130   2012
  Planarity :  0.003   0.027   2040
  Dihedral  :  3.966  22.564   1760
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.72 %
    Favored  : 81.46 %
  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:  3.62 (0.21), residues: 1508
  helix:  2.86 (0.14), residues: 1264
  sheet:  0.56 (0.80), residues: 48
  loop : -0.51 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.007   0.001   TYR C 182 
 PHE   0.014   0.002   PHE B 125 
 TRP   0.006   0.001   TRP D 328 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (12328)
  covalent geometry    : angle       0.44869 (16728)
  hydrogen bonds       : bond        0.04306 ( 1072)
  hydrogen bonds       : angle       4.06600 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7870 (mp0) cc_final: 0.7543 (mp0)
REVERT: A  354 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8303 (mm-30)
REVERT: A  420 ILE cc_start: 0.8763 (mm) cc_final: 0.8547 (mt)
REVERT: B   33 GLU cc_start: 0.7861 (mp0) cc_final: 0.7533 (mp0)
REVERT: B  354 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8307 (mm-30)
REVERT: B  420 ILE cc_start: 0.8817 (mm) cc_final: 0.8561 (mt)
REVERT: C   33 GLU cc_start: 0.7862 (mp0) cc_final: 0.7534 (mp0)
REVERT: C  354 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: C  420 ILE cc_start: 0.8767 (mm) cc_final: 0.8545 (mt)
REVERT: D   33 GLU cc_start: 0.7853 (mp0) cc_final: 0.7528 (mp0)
REVERT: D  354 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8310 (mm-30)
REVERT: D  420 ILE cc_start: 0.8799 (mm) cc_final: 0.8541 (mt)
  outliers start: 24
  outliers final: 12
  residues processed: 188
  average time/residue: 1.4083
  time to fit residues: 287.0988
Evaluate side-chains
  168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 141 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 140 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.137605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.097822 restraints weight = 35797.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.70
r_work: 0.2887 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.0712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12328  Z= 0.181
  Angle     :  0.467   4.288  16728  Z= 0.256
  Chirality :  0.035   0.128   2012
  Planarity :  0.004   0.054   2040
  Dihedral  :  4.066  22.488   1760
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.33 %
    Favored  : 80.85 %
  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:  3.46 (0.21), residues: 1508
  helix:  2.75 (0.14), residues: 1264
  sheet:  0.48 (0.79), residues: 48
  loop : -0.55 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 156 
 TYR   0.009   0.001   TYR C 182 
 PHE   0.011   0.002   PHE A 298 
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12328)
  covalent geometry    : angle       0.46689 (16728)
  hydrogen bonds       : bond        0.04454 ( 1072)
  hydrogen bonds       : angle       4.11434 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7499 (mp0)
REVERT: A  354 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8307 (mm-30)
REVERT: A  420 ILE cc_start: 0.8773 (mm) cc_final: 0.8553 (mt)
REVERT: A  423 GLN cc_start: 0.5932 (mm110) cc_final: 0.4947 (pt0)
REVERT: B   33 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7485 (mp0)
REVERT: B  354 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8316 (mm-30)
REVERT: B  420 ILE cc_start: 0.8810 (mm) cc_final: 0.8567 (mt)
REVERT: B  423 GLN cc_start: 0.5906 (mm110) cc_final: 0.4931 (pt0)
REVERT: C   33 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7483 (mp0)
REVERT: C  354 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8316 (mm-30)
REVERT: C  420 ILE cc_start: 0.8804 (mm) cc_final: 0.8559 (mt)
REVERT: C  423 GLN cc_start: 0.5913 (mm110) cc_final: 0.4929 (pt0)
REVERT: D   33 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7482 (mp0)
REVERT: D  354 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8316 (mm-30)
REVERT: D  420 ILE cc_start: 0.8806 (mm) cc_final: 0.8563 (mt)
REVERT: D  423 GLN cc_start: 0.5922 (mm110) cc_final: 0.4932 (pt0)
  outliers start: 24
  outliers final: 8
  residues processed: 188
  average time/residue: 1.4637
  time to fit residues: 298.0199
Evaluate side-chains
  177 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 169
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 110 optimal weight:    4.9990
   chunk 123 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 122 optimal weight:    0.8980
   chunk 137 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 136 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 102 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9980
   chunk 132 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.139376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.100161 restraints weight = 35796.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.69
r_work: 0.2918 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.0918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12328  Z= 0.124
  Angle     :  0.434   4.200  16728  Z= 0.235
  Chirality :  0.034   0.128   2012
  Planarity :  0.003   0.029   2040
  Dihedral  :  3.698  17.395   1756
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.09 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.71 (0.21), residues: 1508
  helix:  2.93 (0.14), residues: 1264
  sheet:  0.36 (0.82), residues: 48
  loop : -0.45 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 129 
 TYR   0.005   0.001   TYR A 182 
 PHE   0.015   0.001   PHE D 125 
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12328)
  covalent geometry    : angle       0.43363 (16728)
  hydrogen bonds       : bond        0.04045 ( 1072)
  hydrogen bonds       : angle       3.98755 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7486 (mp0)
REVERT: A  354 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: A  420 ILE cc_start: 0.8774 (mm) cc_final: 0.8565 (mt)
REVERT: A  423 GLN cc_start: 0.5938 (mm110) cc_final: 0.4952 (pt0)
REVERT: B   33 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7478 (mp0)
REVERT: B  354 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8185 (mm-30)
REVERT: B  420 ILE cc_start: 0.8784 (mm) cc_final: 0.8569 (mt)
REVERT: B  423 GLN cc_start: 0.5916 (mm110) cc_final: 0.4943 (pt0)
REVERT: C   33 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7494 (mp0)
REVERT: C  354 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8193 (mm-30)
REVERT: C  420 ILE cc_start: 0.8779 (mm) cc_final: 0.8553 (mt)
REVERT: C  423 GLN cc_start: 0.5922 (mm110) cc_final: 0.4942 (pt0)
REVERT: D   33 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7483 (mp0)
REVERT: D  120 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7170 (t160)
REVERT: D  354 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: D  420 ILE cc_start: 0.8783 (mm) cc_final: 0.8558 (mt)
REVERT: D  423 GLN cc_start: 0.5932 (mm110) cc_final: 0.4948 (pt0)
  outliers start: 20
  outliers final: 13
  residues processed: 180
  average time/residue: 1.4355
  time to fit residues: 281.1212
Evaluate side-chains
  175 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue  120 ASN
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 126 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 148 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.137524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.098008 restraints weight = 35928.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.69
r_work: 0.2892 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.0793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12328  Z= 0.179
  Angle     :  0.463   4.365  16728  Z= 0.253
  Chirality :  0.035   0.128   2012
  Planarity :  0.004   0.038   2040
  Dihedral  :  3.810  19.614   1756
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.93 %
    Favored  : 80.24 %
  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:  3.49 (0.21), residues: 1508
  helix:  2.78 (0.14), residues: 1264
  sheet:  0.42 (0.81), residues: 48
  loop : -0.54 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 129 
 TYR   0.009   0.001   TYR B 182 
 PHE   0.011   0.002   PHE B 298 
 TRP   0.006   0.001   TRP D 328 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12328)
  covalent geometry    : angle       0.46296 (16728)
  hydrogen bonds       : bond        0.04395 ( 1072)
  hydrogen bonds       : angle       4.08215 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7452 (mp0)
REVERT: A  354 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: A  420 ILE cc_start: 0.8791 (mm) cc_final: 0.8565 (mt)
REVERT: A  423 GLN cc_start: 0.5987 (mm110) cc_final: 0.4945 (pt0)
REVERT: B   33 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7446 (mp0)
REVERT: B  354 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8324 (mm-30)
REVERT: B  420 ILE cc_start: 0.8805 (mm) cc_final: 0.8561 (mt)
REVERT: B  423 GLN cc_start: 0.5959 (mm110) cc_final: 0.4930 (pt0)
REVERT: C   33 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7451 (mp0)
REVERT: C  354 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8324 (mm-30)
REVERT: C  420 ILE cc_start: 0.8797 (mm) cc_final: 0.8554 (mt)
REVERT: C  423 GLN cc_start: 0.5971 (mm110) cc_final: 0.4928 (pt0)
REVERT: D   33 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7449 (mp0)
REVERT: D  354 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8328 (mm-30)
REVERT: D  420 ILE cc_start: 0.8800 (mm) cc_final: 0.8560 (mt)
REVERT: D  423 GLN cc_start: 0.5978 (mm110) cc_final: 0.4933 (pt0)
  outliers start: 24
  outliers final: 15
  residues processed: 192
  average time/residue: 1.4082
  time to fit residues: 294.4610
Evaluate side-chains
  187 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 135 optimal weight:    7.9990
   chunk 137 optimal weight:    2.9990
   chunk 145 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.3570 r_free = 0.3570 target = 0.136805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.097245 restraints weight = 35846.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.69
r_work: 0.2878 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.0864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12328  Z= 0.210
  Angle     :  0.490   4.643  16728  Z= 0.268
  Chirality :  0.036   0.127   2012
  Planarity :  0.004   0.042   2040
  Dihedral  :  4.034  24.353   1756
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.31 %
    Favored  : 79.86 %
  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:  3.27 (0.21), residues: 1508
  helix:  2.62 (0.14), residues: 1264
  sheet:  0.51 (0.80), residues: 48
  loop : -0.64 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 129 
 TYR   0.009   0.001   TYR C 182 
 PHE   0.023   0.002   PHE C 125 
 TRP   0.007   0.001   TRP B 328 
 HIS   0.004   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (12328)
  covalent geometry    : angle       0.48967 (16728)
  hydrogen bonds       : bond        0.04600 ( 1072)
  hydrogen bonds       : angle       4.18478 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A  354 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8326 (mm-30)
REVERT: A  420 ILE cc_start: 0.8798 (mm) cc_final: 0.8578 (mt)
REVERT: A  423 GLN cc_start: 0.5893 (mm110) cc_final: 0.4864 (pt0)
REVERT: B  354 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8327 (mm-30)
REVERT: B  420 ILE cc_start: 0.8798 (mm) cc_final: 0.8569 (mt)
REVERT: B  423 GLN cc_start: 0.5868 (mm110) cc_final: 0.4842 (pt0)
REVERT: C  354 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8330 (mm-30)
REVERT: C  420 ILE cc_start: 0.8798 (mm) cc_final: 0.8562 (mt)
REVERT: C  423 GLN cc_start: 0.5932 (mm110) cc_final: 0.4877 (pt0)
REVERT: D  354 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8331 (mm-30)
REVERT: D  420 ILE cc_start: 0.8801 (mm) cc_final: 0.8568 (mt)
REVERT: D  423 GLN cc_start: 0.5881 (mm110) cc_final: 0.4846 (pt0)
  outliers start: 24
  outliers final: 15
  residues processed: 196
  average time/residue: 1.4300
  time to fit residues: 305.4682
Evaluate side-chains
  194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 146 optimal weight:    5.9990
   chunk 48 optimal weight:    0.4980
   chunk 116 optimal weight:    5.9990
   chunk 131 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 129 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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 = 0.3587 r_free = 0.3587 target = 0.138343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.098979 restraints weight = 35725.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.69
r_work: 0.2902 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12328  Z= 0.150
  Angle     :  0.453   4.825  16728  Z= 0.247
  Chirality :  0.034   0.129   2012
  Planarity :  0.003   0.031   2040
  Dihedral  :  3.836  20.197   1756
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 18.69 %
    Favored  : 80.17 %
  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:  3.49 (0.21), residues: 1508
  helix:  2.78 (0.14), residues: 1264
  sheet:  0.45 (0.81), residues: 48
  loop : -0.57 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 129 
 TYR   0.007   0.001   TYR B 182 
 PHE   0.011   0.001   PHE C  11 
 TRP   0.007   0.001   TRP B 328 
 HIS   0.004   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12328)
  covalent geometry    : angle       0.45344 (16728)
  hydrogen bonds       : bond        0.04233 ( 1072)
  hydrogen bonds       : angle       4.07946 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   31 ARG cc_start: 0.6424 (ttm-80) cc_final: 0.6177 (ttm-80)
REVERT: A  354 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: A  420 ILE cc_start: 0.8791 (mm) cc_final: 0.8573 (mt)
REVERT: A  423 GLN cc_start: 0.5943 (mm110) cc_final: 0.4888 (pt0)
REVERT: B   31 ARG cc_start: 0.6404 (ttm-80) cc_final: 0.6156 (ttm-80)
REVERT: B  354 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8191 (mm-30)
REVERT: B  420 ILE cc_start: 0.8793 (mm) cc_final: 0.8564 (mt)
REVERT: B  423 GLN cc_start: 0.5967 (mm110) cc_final: 0.4905 (pt0)
REVERT: C   31 ARG cc_start: 0.6401 (ttm-80) cc_final: 0.6150 (ttm-80)
REVERT: C  354 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8198 (mm-30)
REVERT: C  420 ILE cc_start: 0.8785 (mm) cc_final: 0.8557 (mt)
REVERT: C  423 GLN cc_start: 0.5979 (mm110) cc_final: 0.4905 (pt0)
REVERT: D   31 ARG cc_start: 0.6418 (ttm-80) cc_final: 0.6167 (ttm-80)
REVERT: D  120 ASN cc_start: 0.7369 (OUTLIER) cc_final: 0.7153 (t160)
REVERT: D  354 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8195 (mm-30)
REVERT: D  420 ILE cc_start: 0.8789 (mm) cc_final: 0.8562 (mt)
REVERT: D  423 GLN cc_start: 0.5937 (mm110) cc_final: 0.4880 (pt0)
  outliers start: 15
  outliers final: 14
  residues processed: 171
  average time/residue: 1.5395
  time to fit residues: 285.1219
Evaluate side-chains
  174 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue  120 ASN
Chi-restraints excluded: chain D residue  182 TYR
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 144 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.140479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101849 restraints weight = 35657.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.67
r_work: 0.2905 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12328  Z= 0.152
  Angle     :  0.449   4.165  16728  Z= 0.246
  Chirality :  0.034   0.128   2012
  Planarity :  0.003   0.030   2040
  Dihedral  :  3.767  18.453   1756
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 18.62 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.52 (0.21), residues: 1508
  helix:  2.80 (0.14), residues: 1264
  sheet:  0.36 (0.80), residues: 48
  loop : -0.55 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 129 
 TYR   0.007   0.001   TYR C 182 
 PHE   0.021   0.002   PHE A 125 
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12328)
  covalent geometry    : angle       0.44889 (16728)
  hydrogen bonds       : bond        0.04229 ( 1072)
  hydrogen bonds       : angle       4.05589 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   31 ARG cc_start: 0.6400 (ttm-80) cc_final: 0.6156 (ttm-80)
REVERT: A  354 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: A  420 ILE cc_start: 0.8786 (mm) cc_final: 0.8576 (mt)
REVERT: A  423 GLN cc_start: 0.6103 (mm110) cc_final: 0.4979 (pt0)
REVERT: B   31 ARG cc_start: 0.6382 (ttm-80) cc_final: 0.6136 (ttm-80)
REVERT: B  354 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: B  420 ILE cc_start: 0.8762 (mm) cc_final: 0.8536 (mt)
REVERT: B  423 GLN cc_start: 0.6074 (mm110) cc_final: 0.4963 (pt0)
REVERT: C   31 ARG cc_start: 0.6377 (ttm-80) cc_final: 0.6127 (ttm-80)
REVERT: C  354 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8198 (mm-30)
REVERT: C  420 ILE cc_start: 0.8743 (mm) cc_final: 0.8517 (mt)
REVERT: C  423 GLN cc_start: 0.6087 (mm110) cc_final: 0.4964 (pt0)
REVERT: D   31 ARG cc_start: 0.6392 (ttm-80) cc_final: 0.6143 (ttm-80)
REVERT: D  354 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8314 (mm-30)
REVERT: D  420 ILE cc_start: 0.8758 (mm) cc_final: 0.8534 (mt)
REVERT: D  423 GLN cc_start: 0.6099 (mm110) cc_final: 0.4973 (pt0)
  outliers start: 17
  outliers final: 16
  residues processed: 174
  average time/residue: 1.5378
  time to fit residues: 289.2030
Evaluate side-chains
  179 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 130 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.138069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.098666 restraints weight = 35904.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.69
r_work: 0.2896 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12328  Z= 0.166
  Angle     :  0.457   4.061  16728  Z= 0.251
  Chirality :  0.035   0.128   2012
  Planarity :  0.004   0.035   2040
  Dihedral  :  3.793  18.707   1756
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 18.69 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.47 (0.21), residues: 1508
  helix:  2.76 (0.14), residues: 1264
  sheet:  0.38 (0.81), residues: 48
  loop : -0.56 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.008   0.001   TYR C 182 
 PHE   0.011   0.002   PHE A 298 
 TRP   0.007   0.001   TRP A 328 
 HIS   0.004   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12328)
  covalent geometry    : angle       0.45708 (16728)
  hydrogen bonds       : bond        0.04306 ( 1072)
  hydrogen bonds       : angle       4.07144 ( 3204)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A   31 ARG cc_start: 0.6396 (ttm-80) cc_final: 0.6149 (ttm-80)
REVERT: A  354 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: A  423 GLN cc_start: 0.6165 (mm110) cc_final: 0.5008 (pt0)
REVERT: B   31 ARG cc_start: 0.6374 (ttm-80) cc_final: 0.6125 (ttm-80)
REVERT: B  354 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8315 (mm-30)
REVERT: B  420 ILE cc_start: 0.8765 (mm) cc_final: 0.8544 (mt)
REVERT: B  423 GLN cc_start: 0.6137 (mm110) cc_final: 0.4995 (pt0)
REVERT: C   31 ARG cc_start: 0.6372 (ttm-80) cc_final: 0.6120 (ttm-80)
REVERT: C  354 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: C  420 ILE cc_start: 0.8758 (mm) cc_final: 0.8539 (mt)
REVERT: C  423 GLN cc_start: 0.6150 (mm110) cc_final: 0.4997 (pt0)
REVERT: D   31 ARG cc_start: 0.6383 (ttm-80) cc_final: 0.6134 (ttm-80)
REVERT: D  354 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8323 (mm-30)
REVERT: D  420 ILE cc_start: 0.8761 (mm) cc_final: 0.8542 (mt)
REVERT: D  423 GLN cc_start: 0.6160 (mm110) cc_final: 0.5002 (pt0)
  outliers start: 16
  outliers final: 16
  residues processed: 177
  average time/residue: 1.3822
  time to fit residues: 263.9474
Evaluate side-chains
  176 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 148 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.138217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.098848 restraints weight = 35759.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.69
r_work: 0.2896 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12328  Z= 0.165
  Angle     :  0.455   4.040  16728  Z= 0.250
  Chirality :  0.035   0.128   2012
  Planarity :  0.003   0.032   2040
  Dihedral  :  3.789  18.713   1756
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.47 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.47 (0.21), residues: 1508
  helix:  2.76 (0.14), residues: 1264
  sheet:  0.38 (0.81), residues: 48
  loop : -0.56 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.008   0.001   TYR A 182 
 PHE   0.022   0.002   PHE D 125 
 TRP   0.008   0.001   TRP B 328 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12328)
  covalent geometry    : angle       0.45516 (16728)
  hydrogen bonds       : bond        0.04295 ( 1072)
  hydrogen bonds       : angle       4.07029 ( 3204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8983.66 seconds
wall clock time: 153 minutes 1.79 seconds (9181.79 seconds total)