Starting phenix.real_space_refine
on Tue Feb  3 13:08:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fte_50743/02_2026/9fte_50743.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fte_50743/02_2026/9fte_50743.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fte_50743/02_2026/9fte_50743.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fte_50743/02_2026/9fte_50743.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fte_50743/02_2026/9fte_50743.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fte_50743/02_2026/9fte_50743.map"
  }
  resolution = 3.82
  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=   0.010
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      21      5.16       5
     C    1822      2.51       5
     N     462      2.21       5
     O     481      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2786
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2001
          Classifications: {'peptide': 255}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 785
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 0.62, per 1000 atoms: 0.22
  Number of scatterers: 2786
  At special positions: 0
  Unit cell: (52.36, 65.7067, 105.747, 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      21     16.00
     O     481      8.00
     N     462      7.00
     C    1822      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A5963 " - pdb=" SG  CYS A6045 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.14
  Conformation dependent library (CDL) restraints added in 66.1 milliseconds
  

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  672

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 2 sheets defined
      56.4% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5898 through 5901
    Processing helix  chain 'A' and resid 5902 through 5923
      removed outlier: 4.531A  pdb=" N   GLY A5906 " --> pdb=" O   PHE A5902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 5931 through 5952
    Processing helix  chain 'A' and resid 5954 through 5959
    Processing helix  chain 'A' and resid 5962 through 5992
      removed outlier: 3.930A  pdb=" N   GLN A5977 " --> pdb=" O   LEU A5973 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   PHE A5978 " --> pdb=" O   TYR A5974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 5998 through 6001
      removed outlier: 4.038A  pdb=" N   ARG A6001 " --> pdb=" O   HIS A5998 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 5998 through 6001'
    Processing helix  chain 'A' and resid 6002 through 6028
      Proline residue:  A6014  - end of helix
      removed outlier: 4.047A  pdb=" N   ARG A6026 " --> pdb=" O   ILE A6022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6032 through 6037
      removed outlier: 3.669A  pdb=" N   ILE A6036 " --> pdb=" O   SER A6032 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR A6037 " --> pdb=" O   MET A6033 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 6032 through 6037'
    Processing helix  chain 'A' and resid 6049 through 6079
      removed outlier: 5.337A  pdb=" N   VAL A6060 " --> pdb=" O   THR A6056 " (cutoff:3.500A)
      Proline residue:  A6061  - end of helix
    Processing helix  chain 'A' and resid 6096 through 6118
      removed outlier: 3.683A  pdb=" N   SER A6109 " --> pdb=" O   PHE A6105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6124 through 6147
      removed outlier: 3.505A  pdb=" N   VAL A6128 " --> pdb=" O   PHE A6124 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A6147 " --> pdb=" O   VAL A6143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6148 through 6151
      removed outlier: 3.562A  pdb=" N   GLN A6151 " --> pdb=" O   LEU A6148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 6148 through 6151'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39
      removed outlier: 4.714A  pdb=" N   ALA B  51 " --> pdb=" O   TRP B  38 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA B  52 " --> pdb=" O   ASN B  60 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASN B  60 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 74
      removed outlier: 3.505A  pdb=" N   ASP B  74 " --> pdb=" O   THR B  79 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    142 hydrogen bonds defined for protein.
    423 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.23

  Time building geometry restraints manager: 0.19 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: 860
        1.34 -     1.46: 729
        1.46 -     1.58: 1248
        1.58 -     1.70: 1
        1.70 -     1.81: 31
  Bond restraints: 2869
  Sorted by residual:
  bond pdb=" CB  PRO B 106 "
       pdb=" CG  PRO B 106 "
    ideal  model  delta    sigma   weight residual
    1.492  1.580 -0.088 5.00e-02 4.00e+02 3.07e+00
  bond pdb=" CA  PRO A6061 "
       pdb=" C   PRO A6061 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 1.42e-02 4.96e+03 3.02e+00
  bond pdb=" C   VAL A6060 "
       pdb=" O   VAL A6060 "
    ideal  model  delta    sigma   weight residual
    1.242  1.227  0.015 8.60e-03 1.35e+04 2.89e+00
  bond pdb=" C   SER A5959 "
       pdb=" O   SER A5959 "
    ideal  model  delta    sigma   weight residual
    1.239  1.226  0.013 9.60e-03 1.09e+04 1.81e+00
  bond pdb=" C   PRO A6061 "
       pdb=" O   PRO A6061 "
    ideal  model  delta    sigma   weight residual
    1.237  1.225  0.012 1.20e-02 6.94e+03 1.03e+00
  ... (remaining 2864 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 3739
        1.53 -     3.05: 133
        3.05 -     4.58: 25
        4.58 -     6.10: 11
        6.10 -     7.63: 5
  Bond angle restraints: 3913
  Sorted by residual:
  angle pdb=" CA  VAL A6060 "
        pdb=" C   VAL A6060 "
        pdb=" N   PRO A6061 "
      ideal   model   delta    sigma   weight residual
     120.83  117.19    3.64 6.10e-01 2.69e+00 3.55e+01
  angle pdb=" CA  SER A5959 "
        pdb=" C   SER A5959 "
        pdb=" N   GLU A5960 "
      ideal   model   delta    sigma   weight residual
     119.52  115.30    4.22 7.90e-01 1.60e+00 2.86e+01
  angle pdb=" N   GLU A5960 "
        pdb=" CA  GLU A5960 "
        pdb=" C   GLU A5960 "
      ideal   model   delta    sigma   weight residual
     112.58  117.90   -5.32 1.22e+00 6.72e-01 1.90e+01
  angle pdb=" C   VAL A6060 "
        pdb=" CA  VAL A6060 "
        pdb=" CB  VAL A6060 "
      ideal   model   delta    sigma   weight residual
     114.00  108.43    5.57 1.31e+00 5.83e-01 1.81e+01
  angle pdb=" C   SER A5959 "
        pdb=" CA  SER A5959 "
        pdb=" CB  SER A5959 "
      ideal   model   delta    sigma   weight residual
     116.54  112.47    4.07 1.15e+00 7.56e-01 1.25e+01
  ... (remaining 3908 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 1362
       16.45 -    32.89: 196
       32.89 -    49.34: 64
       49.34 -    65.78: 6
       65.78 -    82.23: 5
  Dihedral angle restraints: 1633
    sinusoidal: 580
      harmonic: 1053
  Sorted by residual:
  dihedral pdb=" CB  CYS A5963 "
           pdb=" SG  CYS A5963 "
           pdb=" SG  CYS A6045 "
           pdb=" CB  CYS A6045 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -42.08  -43.92     1      1.00e+01 1.00e-02 2.69e+01
  dihedral pdb=" C   GLU A5960 "
           pdb=" N   GLU A5960 "
           pdb=" CA  GLU A5960 "
           pdb=" CB  GLU A5960 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.47   10.87     0      2.50e+00 1.60e-01 1.89e+01
  dihedral pdb=" N   GLU A5960 "
           pdb=" C   GLU A5960 "
           pdb=" CA  GLU A5960 "
           pdb=" CB  GLU A5960 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.15  -10.35     0      2.50e+00 1.60e-01 1.71e+01
  ... (remaining 1630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 411
       0.090 -    0.180: 21
       0.180 -    0.271: 1
       0.271 -    0.361: 0
       0.361 -    0.451: 1
  Chirality restraints: 434
  Sorted by residual:
  chirality pdb=" CA  GLU A5960 "
            pdb=" N   GLU A5960 "
            pdb=" C   GLU A5960 "
            pdb=" CB  GLU A5960 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.08e+00
  chirality pdb=" CA  PRO A6061 "
            pdb=" N   PRO A6061 "
            pdb=" C   PRO A6061 "
            pdb=" CB  PRO A6061 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CB  ILE A6047 "
            pdb=" CA  ILE A6047 "
            pdb=" CG1 ILE A6047 "
            pdb=" CG2 ILE A6047 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 431 not shown)

  Planarity restraints: 486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A5957 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   HIS A5957 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   HIS A5957 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LEU A5958 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A6060 "    0.053 5.00e-02 4.00e+02   8.06e-02 1.04e+01
        pdb=" N   PRO A6061 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A6061 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A6061 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A6105 "    0.016 2.00e-02 2.50e+03   1.28e-02 2.87e+00
        pdb=" CG  PHE A6105 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A6105 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A6105 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A6105 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A6105 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A6105 "    0.004 2.00e-02 2.50e+03
  ... (remaining 483 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 27
        2.58 -     3.16: 2422
        3.16 -     3.74: 4361
        3.74 -     4.32: 5212
        4.32 -     4.90: 8448
  Nonbonded interactions: 20470
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A5945 "
            pdb=" CZ2 TRP A6112 "
     model   vdw
     1.999 3.340
  nonbonded pdb=" OD2 ASP B  91 "
            pdb=" OH  TYR B  95 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" OG  SER A5955 "
            pdb=" O   ASP A6043 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" O   ASN B  34 "
            pdb=" NH2 ARG B  73 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OD1 ASN B  34 "
            pdb=" N   ALA B  35 "
     model   vdw
     2.294 3.120
  ... (remaining 20465 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.110
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
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   0.088   2871  Z= 0.190
  Angle     :  0.755   7.626   3917  Z= 0.446
  Chirality :  0.049   0.451    434
  Planarity :  0.006   0.081    486
  Dihedral  : 17.456  82.226    955
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 18.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 37.10 %
    Favored  : 62.19 %
  Cbeta Deviations :  0.30 %
  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 are not related in a simple way.
  whole: -0.24 (0.46), residues: 358
  helix:  1.55 (0.39), residues: 183
  sheet: -5.55 (0.51), residues: 17
  loop : -1.64 (0.48), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  55 
 TYR   0.012   0.001   TYR A6121 
 PHE   0.029   0.002   PHE A6105 
 TRP   0.020   0.002   TRP A5989 
 HIS   0.002   0.001   HIS A6118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 2869)
  covalent geometry    : angle       0.75510 ( 3913)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.41756 (    4)
  hydrogen bonds       : bond        0.11068 (  142)
  hydrogen bonds       : angle       5.33561 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 5960 GLU cc_start: 0.4647 (OUTLIER) cc_final: 0.4444 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0588
  time to fit residues: 3.6955
Evaluate side-chains
  45 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5960 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.173842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.155545 restraints weight = 6082.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.158952 restraints weight = 3710.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.161333 restraints weight = 2553.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.163157 restraints weight = 1935.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.164117 restraints weight = 1536.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6381
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   2871  Z= 0.166
  Angle     :  0.665   6.795   3917  Z= 0.348
  Chirality :  0.041   0.126    434
  Planarity :  0.004   0.023    486
  Dihedral  :  4.959  27.430    396
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 32.51 %
    Favored  : 61.48 %
  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 are not related in a simple way.
  whole: -0.17 (0.47), residues: 358
  helix:  1.60 (0.40), residues: 188
  sheet: -4.31 (0.69), residues: 33
  loop : -1.44 (0.55), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  55 
 TYR   0.013   0.001   TYR B  96 
 PHE   0.029   0.002   PHE A6105 
 TRP   0.010   0.002   TRP A5989 
 HIS   0.003   0.001   HIS A5957 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2869)
  covalent geometry    : angle       0.66513 ( 3913)
  SS BOND              : bond        0.00038 (    2)
  SS BOND              : angle       0.72202 (    4)
  hydrogen bonds       : bond        0.06117 (  142)
  hydrogen bonds       : angle       4.14023 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 6046 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.6020 (t80)
REVERT: A 6069 PHE cc_start: 0.5777 (OUTLIER) cc_final: 0.5497 (t80)
REVERT: A 6076 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7252 (m-80)
REVERT: A 6082 TRP cc_start: 0.6709 (p90) cc_final: 0.6395 (p90)
  outliers start: 17
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0327
  time to fit residues: 2.3374
Evaluate side-chains
  55 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6069 PHE
Chi-restraints excluded: chain A residue 6076 TYR
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0070
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.175162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.157182 restraints weight = 6085.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.160284 restraints weight = 3853.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.162580 restraints weight = 2722.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.164420 restraints weight = 2077.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.165399 restraints weight = 1659.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   2871  Z= 0.141
  Angle     :  0.627   7.026   3917  Z= 0.323
  Chirality :  0.041   0.128    434
  Planarity :  0.003   0.022    486
  Dihedral  :  4.567  19.098    393
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  9.54 %
    Allowed  : 29.68 %
    Favored  : 60.78 %
  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 are not related in a simple way.
  whole: -0.03 (0.47), residues: 358
  helix:  2.01 (0.40), residues: 179
  sheet: -4.54 (0.63), residues: 33
  loop : -1.53 (0.52), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  55 
 TYR   0.012   0.001   TYR B  96 
 PHE   0.016   0.001   PHE A6105 
 TRP   0.010   0.001   TRP A5989 
 HIS   0.002   0.001   HIS A6118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 2869)
  covalent geometry    : angle       0.62696 ( 3913)
  SS BOND              : bond        0.00111 (    2)
  SS BOND              : angle       0.54496 (    4)
  hydrogen bonds       : bond        0.05604 (  142)
  hydrogen bonds       : angle       3.96140 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 44
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A 5921 MET cc_start: 0.6703 (tmm) cc_final: 0.6348 (tmm)
REVERT: A 6046 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5914 (t80)
REVERT: A 6069 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5550 (t80)
REVERT: A 6105 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6589 (t80)
REVERT: B   31 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6116 (p90)
  outliers start: 27
  outliers final: 13
  residues processed: 65
  average time/residue: 0.0312
  time to fit residues: 2.7990
Evaluate side-chains
  57 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5907 LEU
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6069 PHE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0000
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
A5971 HIS
A6094 ASN
B  83 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.175380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.156881 restraints weight = 6192.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.160230 restraints weight = 3799.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.162733 restraints weight = 2610.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.164274 restraints weight = 1950.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.165693 restraints weight = 1571.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6380
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2871  Z= 0.153
  Angle     :  0.666   7.831   3917  Z= 0.337
  Chirality :  0.041   0.128    434
  Planarity :  0.003   0.022    486
  Dihedral  :  4.600  19.560    393
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  9.54 %
    Allowed  : 31.10 %
    Favored  : 59.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.47), residues: 358
  helix:  2.00 (0.40), residues: 180
  sheet: -5.68 (0.49), residues: 17
  loop : -1.56 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  40 
 TYR   0.012   0.001   TYR B  96 
 PHE   0.022   0.002   PHE A6105 
 TRP   0.016   0.002   TRP A6082 
 HIS   0.002   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2869)
  covalent geometry    : angle       0.66664 ( 3913)
  SS BOND              : bond        0.00112 (    2)
  SS BOND              : angle       0.51414 (    4)
  hydrogen bonds       : bond        0.05832 (  142)
  hydrogen bonds       : angle       3.99016 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 43
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A 5921 MET cc_start: 0.6948 (tmm) cc_final: 0.6490 (tmm)
REVERT: A 6046 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5990 (t80)
REVERT: A 6076 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7344 (m-10)
REVERT: A 6082 TRP cc_start: 0.6850 (p90) cc_final: 0.6468 (p90)
REVERT: A 6105 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6802 (t80)
REVERT: B   31 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6150 (p90)
  outliers start: 27
  outliers final: 19
  residues processed: 65
  average time/residue: 0.0267
  time to fit residues: 2.3816
Evaluate side-chains
  65 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 42
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5907 LEU
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5934 LEU
Chi-restraints excluded: chain A residue 5975 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5993 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6033 MET
Chi-restraints excluded: chain A residue 6045 CYS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6076 TYR
Chi-restraints excluded: chain A residue 6101 ILE
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6121 TYR
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0970
   chunk 5 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.175670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.157255 restraints weight = 6011.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.160630 restraints weight = 3656.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.162904 restraints weight = 2507.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.164843 restraints weight = 1913.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.166141 restraints weight = 1510.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6364
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2871  Z= 0.141
  Angle     :  0.642   8.123   3917  Z= 0.324
  Chirality :  0.040   0.128    434
  Planarity :  0.003   0.022    486
  Dihedral  :  4.519  19.337    393
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  9.54 %
    Allowed  : 32.51 %
    Favored  : 57.95 %
  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 are not related in a simple way.
  whole:  0.19 (0.47), residues: 358
  helix:  2.14 (0.40), residues: 179
  sheet: -4.29 (0.75), residues: 24
  loop : -1.63 (0.51), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  55 
 TYR   0.012   0.001   TYR B  96 
 PHE   0.020   0.001   PHE A6105 
 TRP   0.012   0.002   TRP A5989 
 HIS   0.005   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2869)
  covalent geometry    : angle       0.64262 ( 3913)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.39984 (    4)
  hydrogen bonds       : bond        0.05575 (  142)
  hydrogen bonds       : angle       3.90066 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 47
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A 5921 MET cc_start: 0.7233 (tmm) cc_final: 0.6853 (tmm)
REVERT: A 6046 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6044 (t80)
REVERT: A 6069 PHE cc_start: 0.6225 (t80) cc_final: 0.5489 (m-10)
REVERT: A 6076 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7295 (m-80)
REVERT: A 6082 TRP cc_start: 0.6770 (p90) cc_final: 0.6473 (p90)
REVERT: A 6105 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6784 (t80)
REVERT: B   31 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6158 (p90)
  outliers start: 27
  outliers final: 15
  residues processed: 70
  average time/residue: 0.0449
  time to fit residues: 4.0033
Evaluate side-chains
  64 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5934 LEU
Chi-restraints excluded: chain A residue 5975 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5993 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6047 ILE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6076 TYR
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0270
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN
B  83 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.174421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.156522 restraints weight = 6086.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.159804 restraints weight = 3767.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.162277 restraints weight = 2615.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.163551 restraints weight = 1964.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.164925 restraints weight = 1624.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.4290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2871  Z= 0.139
  Angle     :  0.663   8.268   3917  Z= 0.330
  Chirality :  0.041   0.129    434
  Planarity :  0.003   0.021    486
  Dihedral  :  4.513  19.316    393
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  9.19 %
    Allowed  : 32.51 %
    Favored  : 58.30 %
  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 are not related in a simple way.
  whole:  0.23 (0.47), residues: 358
  helix:  2.18 (0.40), residues: 179
  sheet: -6.00 (0.41), residues: 12
  loop : -1.74 (0.48), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  21 
 TYR   0.012   0.001   TYR B  81 
 PHE   0.022   0.001   PHE A6105 
 TRP   0.013   0.001   TRP A5989 
 HIS   0.005   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 2869)
  covalent geometry    : angle       0.66350 ( 3913)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.36664 (    4)
  hydrogen bonds       : bond        0.05456 (  142)
  hydrogen bonds       : angle       3.87135 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 46
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A 5921 MET cc_start: 0.7231 (tmm) cc_final: 0.6999 (tmm)
REVERT: A 5996 ASP cc_start: 0.8131 (t0) cc_final: 0.7850 (t0)
REVERT: A 6046 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6010 (t80)
REVERT: A 6069 PHE cc_start: 0.6179 (t80) cc_final: 0.5398 (m-10)
REVERT: B   31 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6251 (p90)
  outliers start: 26
  outliers final: 20
  residues processed: 68
  average time/residue: 0.0347
  time to fit residues: 3.1698
Evaluate side-chains
  65 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5934 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5992 LEU
Chi-restraints excluded: chain A residue 5993 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6041 HIS
Chi-restraints excluded: chain A residue 6045 CYS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6047 ILE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6101 ILE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6127 LEU
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A6035 GLN
A6094 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.173818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.155192 restraints weight = 6125.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.158427 restraints weight = 3829.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.160684 restraints weight = 2684.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.162619 restraints weight = 2048.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.163766 restraints weight = 1631.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6425
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2871  Z= 0.158
  Angle     :  0.690   9.744   3917  Z= 0.346
  Chirality :  0.042   0.131    434
  Planarity :  0.003   0.022    486
  Dihedral  :  4.641  19.523    393
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers : 11.66 %
    Allowed  : 31.45 %
    Favored  : 56.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.48), residues: 358
  helix:  2.14 (0.41), residues: 179
  sheet: -4.54 (0.67), residues: 29
  loop : -1.62 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  21 
 TYR   0.016   0.002   TYR B  81 
 PHE   0.033   0.002   PHE A6105 
 TRP   0.019   0.002   TRP A6082 
 HIS   0.004   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2869)
  covalent geometry    : angle       0.69041 ( 3913)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.45027 (    4)
  hydrogen bonds       : bond        0.05835 (  142)
  hydrogen bonds       : angle       3.97729 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 47
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
REVERT: A 5921 MET cc_start: 0.7193 (tmm) cc_final: 0.6915 (tmm)
REVERT: A 5973 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6799 (mp)
REVERT: A 5996 ASP cc_start: 0.8158 (t0) cc_final: 0.7870 (t0)
REVERT: A 6046 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.5997 (t80)
REVERT: A 6069 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.5529 (t80)
REVERT: A 6076 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7331 (m-80)
REVERT: A 6082 TRP cc_start: 0.6768 (p90) cc_final: 0.6520 (p90)
REVERT: A 6105 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6796 (t80)
REVERT: B   31 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6210 (p90)
  outliers start: 33
  outliers final: 23
  residues processed: 74
  average time/residue: 0.0300
  time to fit residues: 2.9371
Evaluate side-chains
  75 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 46
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5907 LEU
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5934 LEU
Chi-restraints excluded: chain A residue 5973 LEU
Chi-restraints excluded: chain A residue 5975 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5992 LEU
Chi-restraints excluded: chain A residue 5993 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6041 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6047 ILE
Chi-restraints excluded: chain A residue 6069 PHE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6076 TYR
Chi-restraints excluded: chain A residue 6101 ILE
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6121 TYR
Chi-restraints excluded: chain A residue 6127 LEU
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain A residue 6148 LEU
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.175767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.156791 restraints weight = 6308.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.160354 restraints weight = 3835.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.162563 restraints weight = 2635.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.164522 restraints weight = 2011.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.165735 restraints weight = 1603.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2871  Z= 0.136
  Angle     :  0.677   8.521   3917  Z= 0.333
  Chirality :  0.041   0.131    434
  Planarity :  0.003   0.023    486
  Dihedral  :  4.593  19.230    393
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  8.83 %
    Allowed  : 33.92 %
    Favored  : 57.24 %
  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 are not related in a simple way.
  whole:  0.24 (0.48), residues: 358
  helix:  2.17 (0.41), residues: 180
  sheet: -6.27 (0.30), residues: 12
  loop : -1.71 (0.49), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.012   0.001   TYR B  81 
 PHE   0.027   0.001   PHE A6105 
 TRP   0.018   0.002   TRP A5989 
 HIS   0.006   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2869)
  covalent geometry    : angle       0.67693 ( 3913)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       0.31402 (    4)
  hydrogen bonds       : bond        0.05419 (  142)
  hydrogen bonds       : angle       3.85590 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 47
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A 5973 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6814 (mp)
REVERT: A 5996 ASP cc_start: 0.8210 (t0) cc_final: 0.7950 (t0)
REVERT: A 6046 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5999 (t80)
REVERT: A 6105 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6581 (t80)
REVERT: B   31 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6181 (p90)
REVERT: B   96 TYR cc_start: 0.6583 (p90) cc_final: 0.4276 (p90)
  outliers start: 25
  outliers final: 18
  residues processed: 69
  average time/residue: 0.0328
  time to fit residues: 3.1608
Evaluate side-chains
  67 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 45
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5934 LEU
Chi-restraints excluded: chain A residue 5973 LEU
Chi-restraints excluded: chain A residue 5975 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6041 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6047 ILE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6101 ILE
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6127 LEU
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain A residue 6148 LEU
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0070
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.175608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.156589 restraints weight = 6302.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.160104 restraints weight = 3873.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.162340 restraints weight = 2670.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.164373 restraints weight = 2040.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.165750 restraints weight = 1615.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6371
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2871  Z= 0.143
  Angle     :  0.704  10.306   3917  Z= 0.347
  Chirality :  0.042   0.159    434
  Planarity :  0.003   0.023    486
  Dihedral  :  4.534  19.208    393
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers : 10.25 %
    Allowed  : 33.22 %
    Favored  : 56.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.48), residues: 358
  helix:  2.22 (0.41), residues: 177
  sheet: -4.74 (0.63), residues: 29
  loop : -1.64 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.011   0.001   TYR B  96 
 PHE   0.028   0.001   PHE A6105 
 TRP   0.027   0.002   TRP A6082 
 HIS   0.006   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 2869)
  covalent geometry    : angle       0.70421 ( 3913)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       0.40851 (    4)
  hydrogen bonds       : bond        0.05563 (  142)
  hydrogen bonds       : angle       3.93861 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 45
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A 5973 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6825 (mp)
REVERT: A 5996 ASP cc_start: 0.8170 (t0) cc_final: 0.7913 (t0)
REVERT: A 6046 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: A 6069 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5587 (t80)
REVERT: A 6076 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7294 (m-80)
REVERT: A 6105 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6752 (t80)
REVERT: B   31 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6290 (p90)
REVERT: B   96 TYR cc_start: 0.6512 (p90) cc_final: 0.4168 (p90)
  outliers start: 29
  outliers final: 20
  residues processed: 70
  average time/residue: 0.0310
  time to fit residues: 3.0445
Evaluate side-chains
  70 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 44
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5907 LEU
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5973 LEU
Chi-restraints excluded: chain A residue 5975 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5992 LEU
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6041 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6047 ILE
Chi-restraints excluded: chain A residue 6069 PHE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6076 TYR
Chi-restraints excluded: chain A residue 6101 ILE
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6127 LEU
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain A residue 6148 LEU
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.172663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.154461 restraints weight = 6148.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.157570 restraints weight = 3869.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.159564 restraints weight = 2732.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.161464 restraints weight = 2126.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.162107 restraints weight = 1705.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6462
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2871  Z= 0.155
  Angle     :  0.708   7.589   3917  Z= 0.350
  Chirality :  0.042   0.129    434
  Planarity :  0.003   0.025    486
  Dihedral  :  4.565  19.290    393
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  9.89 %
    Allowed  : 33.57 %
    Favored  : 56.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.48), residues: 358
  helix:  2.12 (0.41), residues: 178
  sheet: -4.73 (0.64), residues: 29
  loop : -1.58 (0.53), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.012   0.001   TYR B  96 
 PHE   0.029   0.002   PHE A6105 
 TRP   0.020   0.002   TRP A5989 
 HIS   0.005   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2869)
  covalent geometry    : angle       0.70778 ( 3913)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.46137 (    4)
  hydrogen bonds       : bond        0.05939 (  142)
  hydrogen bonds       : angle       4.03265 (  423)

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

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

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  716 Ramachandran restraints generated.
    358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 46
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A 5921 MET cc_start: 0.6719 (tmm) cc_final: 0.6324 (tmm)
REVERT: A 5973 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6791 (mp)
REVERT: A 5996 ASP cc_start: 0.8132 (t0) cc_final: 0.7899 (t0)
REVERT: A 6046 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5950 (t80)
REVERT: A 6069 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5487 (t80)
REVERT: A 6076 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7188 (m-80)
REVERT: A 6105 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6989 (t80)
REVERT: B   31 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6374 (p90)
  outliers start: 28
  outliers final: 21
  residues processed: 70
  average time/residue: 0.0361
  time to fit residues: 3.4503
Evaluate side-chains
  73 residues out of total 305 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 46
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 5907 LEU
Chi-restraints excluded: chain A residue 5910 ILE
Chi-restraints excluded: chain A residue 5918 VAL
Chi-restraints excluded: chain A residue 5973 LEU
Chi-restraints excluded: chain A residue 5975 LEU
Chi-restraints excluded: chain A residue 5986 VAL
Chi-restraints excluded: chain A residue 5992 LEU
Chi-restraints excluded: chain A residue 5998 HIS
Chi-restraints excluded: chain A residue 6041 HIS
Chi-restraints excluded: chain A residue 6046 PHE
Chi-restraints excluded: chain A residue 6047 ILE
Chi-restraints excluded: chain A residue 6069 PHE
Chi-restraints excluded: chain A residue 6071 VAL
Chi-restraints excluded: chain A residue 6076 TYR
Chi-restraints excluded: chain A residue 6094 ASN
Chi-restraints excluded: chain A residue 6101 ILE
Chi-restraints excluded: chain A residue 6105 PHE
Chi-restraints excluded: chain A residue 6108 ILE
Chi-restraints excluded: chain A residue 6113 LEU
Chi-restraints excluded: chain A residue 6127 LEU
Chi-restraints excluded: chain A residue 6128 VAL
Chi-restraints excluded: chain A residue 6148 LEU
Chi-restraints excluded: chain B residue   31 PHE
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  108 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0570
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 11 optimal weight:    0.1980
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
A6094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.174344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.156133 restraints weight = 5935.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.159211 restraints weight = 3749.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.161594 restraints weight = 2646.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.163034 restraints weight = 2011.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.164413 restraints weight = 1654.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6388
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2871  Z= 0.139
  Angle     :  0.709  10.770   3917  Z= 0.344
  Chirality :  0.042   0.131    434
  Planarity :  0.003   0.024    486
  Dihedral  :  4.507  18.981    393
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  9.54 %
    Allowed  : 34.28 %
    Favored  : 56.18 %
  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 are not related in a simple way.
  whole:  0.09 (0.48), residues: 358
  helix:  2.16 (0.40), residues: 178
  sheet: -4.76 (0.62), residues: 29
  loop : -1.57 (0.53), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.011   0.001   TYR B  96 
 PHE   0.028   0.001   PHE A6105 
 TRP   0.025   0.002   TRP A6082 
 HIS   0.006   0.001   HIS A5971 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2869)
  covalent geometry    : angle       0.70965 ( 3913)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       0.42838 (    4)
  hydrogen bonds       : bond        0.05550 (  142)
  hydrogen bonds       : angle       3.93670 (  423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 636.41 seconds
wall clock time: 11 minutes 36.13 seconds (696.13 seconds total)