Starting phenix.real_space_refine
on Sun Jul 27 22:43:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxt_15016/07_2025/7zxt_15016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxt_15016/07_2025/7zxt_15016.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxt_15016/07_2025/7zxt_15016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxt_15016/07_2025/7zxt_15016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxt_15016/07_2025/7zxt_15016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxt_15016/07_2025/7zxt_15016.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001
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      90      5.16       5
     C    6534      2.51       5
     N    1668      2.21       5
     O    1632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9924
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1654
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.66, per 1000 atoms: 0.47
  Number of scatterers: 9924
  At special positions: 0
  Unit cell: (105.294, 101.37, 91.56, 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      90     16.00
     O    1632      8.00
     N    1668      7.00
     C    6534      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 168 " 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: 2.74
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2376

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      72.4% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
    Processing helix  chain 'A' and resid 23 through 42
      removed outlier: 3.608A  pdb=" N   VAL A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 23 through 42
      removed outlier: 3.608A  pdb=" N   VAL B  27 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 10
    Processing helix  chain 'C' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL C  27 " --> pdb=" O   VAL C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 10
    Processing helix  chain 'D' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL D  27 " --> pdb=" O   VAL D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 10
    Processing helix  chain 'E' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL E  27 " --> pdb=" O   VAL E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 10
    Processing helix  chain 'F' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL F  27 " --> pdb=" O   VAL F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE F 180 " --> pdb=" O   ILE F  52 " (cutoff:3.500A)

    751 hydrogen bonds defined for protein.
    2235 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.93

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3006
        1.35 -     1.47: 2751
        1.47 -     1.60: 4293
        1.60 -     1.72: 0
        1.72 -     1.84: 132
  Bond restraints: 10182
  Sorted by residual:
  bond pdb=" C   THR B  86 "
       pdb=" N   PRO B  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.64e+00
  bond pdb=" C   THR E  86 "
       pdb=" N   PRO E  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.64e+00
  bond pdb=" C   THR F  86 "
       pdb=" N   PRO F  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.62e+00
  bond pdb=" C   THR D  86 "
       pdb=" N   PRO D  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.47e+00
  bond pdb=" C   THR C  86 "
       pdb=" N   PRO C  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.42e+00
  ... (remaining 10177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 13433
        1.47 -     2.93: 331
        2.93 -     4.40: 54
        4.40 -     5.87: 30
        5.87 -     7.34: 12
  Bond angle restraints: 13860
  Sorted by residual:
  angle pdb=" N   ILE A  20 "
        pdb=" CA  ILE A  20 "
        pdb=" C   ILE A  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.02    4.10 8.40e-01 1.42e+00 2.38e+01
  angle pdb=" N   ILE D  20 "
        pdb=" CA  ILE D  20 "
        pdb=" C   ILE D  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.06    4.06 8.40e-01 1.42e+00 2.34e+01
  angle pdb=" N   ILE E  20 "
        pdb=" CA  ILE E  20 "
        pdb=" C   ILE E  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.06    4.06 8.40e-01 1.42e+00 2.34e+01
  angle pdb=" N   ILE C  20 "
        pdb=" CA  ILE C  20 "
        pdb=" C   ILE C  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.07    4.05 8.40e-01 1.42e+00 2.33e+01
  angle pdb=" N   ILE F  20 "
        pdb=" CA  ILE F  20 "
        pdb=" C   ILE F  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.07    4.05 8.40e-01 1.42e+00 2.33e+01
  ... (remaining 13855 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 5409
       14.98 -    29.96: 440
       29.96 -    44.94: 127
       44.94 -    59.92: 12
       59.92 -    74.90: 6
  Dihedral angle restraints: 5994
    sinusoidal: 2340
      harmonic: 3654
  Sorted by residual:
  dihedral pdb=" CA  CYS E 179 "
           pdb=" C   CYS E 179 "
           pdb=" N   PHE E 180 "
           pdb=" CA  PHE E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.79  -30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  CYS B 179 "
           pdb=" C   CYS B 179 "
           pdb=" N   PHE B 180 "
           pdb=" CA  PHE B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.79  -30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  CYS F 179 "
           pdb=" C   CYS F 179 "
           pdb=" N   PHE F 180 "
           pdb=" CA  PHE F 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.81  -30.19     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 5991 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1157
       0.041 -    0.081: 399
       0.081 -    0.122: 64
       0.122 -    0.162: 6
       0.162 -    0.203: 18
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  VAL F  13 "
            pdb=" CA  VAL F  13 "
            pdb=" CG1 VAL F  13 "
            pdb=" CG2 VAL F  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL D  13 "
            pdb=" CA  VAL D  13 "
            pdb=" CG1 VAL D  13 "
            pdb=" CG2 VAL D  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  VAL A  13 "
            pdb=" CA  VAL A  13 "
            pdb=" CG1 VAL A  13 "
            pdb=" CG2 VAL A  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F 183 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.48e+00
        pdb=" N   PRO F 184 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO F 184 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F 184 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 183 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 184 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 184 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 184 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 183 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO C 184 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 184 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 184 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 126
        2.70 -     3.25: 10088
        3.25 -     3.80: 16732
        3.80 -     4.35: 19610
        4.35 -     4.90: 33380
  Nonbonded interactions: 79936
  Sorted by model distance:
  nonbonded pdb=" O   ILE E  71 "
            pdb=" OH  TYR E 157 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   ILE C  71 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ILE D  71 "
            pdb=" OH  TYR D 157 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ILE B  71 "
            pdb=" OH  TYR B 157 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ILE F  71 "
            pdb=" OH  TYR F 157 "
     model   vdw
     2.148 3.040
  ... (remaining 79931 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.100
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10200  Z= 0.148
  Angle     :  0.636   7.337  13896  Z= 0.367
  Chirality :  0.043   0.203   1644
  Planarity :  0.003   0.030   1662
  Dihedral  : 12.065  74.901   3564
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.47 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.83 (0.24), residues: 1212
  helix:  3.93 (0.15), residues: 876
  sheet:  1.68 (0.55), residues: 60
  loop : -2.43 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  44 
 HIS   0.002   0.000   HIS C  97 
 PHE   0.008   0.001   PHE E  51 
 TYR   0.007   0.001   TYR B 135 
 ARG   0.002   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07917 (  751)
  hydrogen bonds       : angle       3.36008 ( 2235)
  SS BOND              : bond        0.00711 (   18)
  SS BOND              : angle       2.33027 (   36)
  covalent geometry    : bond        0.00294 (10182)
  covalent geometry    : angle       0.62580 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.146 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 1.3209
  time to fit residues: 337.0841
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  99 GLN
D  97 HIS
E  99 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.092543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.063899 restraints weight = 19850.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.35
r_work: 0.2743 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048  10200  Z= 0.331
  Angle     :  0.721  10.875  13896  Z= 0.376
  Chirality :  0.047   0.176   1644
  Planarity :  0.004   0.042   1662
  Dihedral  :  4.823  31.909   1350
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.47 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.68 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.07 (0.23), residues: 1212
  helix:  3.39 (0.14), residues: 876
  sheet:  0.42 (0.57), residues: 72
  loop : -2.66 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  77 
 HIS   0.011   0.002   HIS B 123 
 PHE   0.013   0.002   PHE F  68 
 TYR   0.012   0.002   TYR B 151 
 ARG   0.003   0.001   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04922 (  751)
  hydrogen bonds       : angle       3.35295 ( 2235)
  SS BOND              : bond        0.01105 (   18)
  SS BOND              : angle       2.61516 (   36)
  covalent geometry    : bond        0.00797 (10182)
  covalent geometry    : angle       0.70914 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 1.230 
Fit side-chains
REVERT: C  153 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8566 (t80)
REVERT: F  153 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8569 (t80)
  outliers start: 36
  outliers final: 16
  residues processed: 183
  average time/residue: 1.4722
  time to fit residues: 286.4174
Evaluate side-chains
  171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  153 PHE
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  217 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.097994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.069232 restraints weight = 20046.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.43
r_work: 0.2850 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10200  Z= 0.121
  Angle     :  0.558   7.604  13896  Z= 0.293
  Chirality :  0.039   0.155   1644
  Planarity :  0.003   0.016   1662
  Dihedral  :  4.134  28.819   1350
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.22 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.21 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.86 (0.24), residues: 1212
  helix:  4.01 (0.14), residues: 882
  sheet:  1.34 (0.51), residues: 60
  loop : -2.74 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 132 
 HIS   0.010   0.001   HIS E 123 
 PHE   0.011   0.001   PHE B  31 
 TYR   0.006   0.001   TYR E 171 
 ARG   0.003   0.000   ARG D  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (  751)
  hydrogen bonds       : angle       3.02206 ( 2235)
  SS BOND              : bond        0.00815 (   18)
  SS BOND              : angle       1.66886 (   36)
  covalent geometry    : bond        0.00273 (10182)
  covalent geometry    : angle       0.55262 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8346 (m-30) cc_final: 0.8112 (m-30)
REVERT: A   99 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: B   66 ASP cc_start: 0.8231 (m-30) cc_final: 0.7993 (m-30)
REVERT: C   66 ASP cc_start: 0.8234 (m-30) cc_final: 0.7995 (m-30)
REVERT: D   66 ASP cc_start: 0.8348 (m-30) cc_final: 0.8115 (m-30)
REVERT: D   99 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: E   66 ASP cc_start: 0.8230 (m-30) cc_final: 0.8002 (m-30)
REVERT: F   66 ASP cc_start: 0.8241 (m-30) cc_final: 0.8004 (m-30)
  outliers start: 21
  outliers final: 8
  residues processed: 176
  average time/residue: 1.3291
  time to fit residues: 249.4455
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain B residue  126 HIS
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  126 HIS
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.097424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.068378 restraints weight = 19819.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.41
r_work: 0.2838 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10200  Z= 0.136
  Angle     :  0.557   8.176  13896  Z= 0.294
  Chirality :  0.040   0.153   1644
  Planarity :  0.003   0.014   1662
  Dihedral  :  4.114  27.631   1350
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.48 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.92 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.77 (0.24), residues: 1212
  helix:  3.94 (0.15), residues: 882
  sheet:  1.16 (0.51), residues: 60
  loop : -2.71 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 132 
 HIS   0.001   0.001   HIS A  97 
 PHE   0.009   0.001   PHE E 180 
 TYR   0.008   0.001   TYR D 171 
 ARG   0.003   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  751)
  hydrogen bonds       : angle       3.01223 ( 2235)
  SS BOND              : bond        0.00783 (   18)
  SS BOND              : angle       1.65763 (   36)
  covalent geometry    : bond        0.00315 (10182)
  covalent geometry    : angle       0.55179 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 1.082 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8350 (m-30) cc_final: 0.8139 (m-30)
REVERT: A   99 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7613 (tm130)
REVERT: A  219 ARG cc_start: 0.1947 (OUTLIER) cc_final: 0.0992 (ttt180)
REVERT: B   66 ASP cc_start: 0.8229 (m-30) cc_final: 0.8014 (m-30)
REVERT: B   99 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7527 (tm130)
REVERT: B  219 ARG cc_start: 0.1916 (OUTLIER) cc_final: 0.0878 (ttt180)
REVERT: C   66 ASP cc_start: 0.8272 (m-30) cc_final: 0.8035 (m-30)
REVERT: C  219 ARG cc_start: 0.2098 (OUTLIER) cc_final: 0.1104 (ttt180)
REVERT: D   66 ASP cc_start: 0.8354 (m-30) cc_final: 0.8146 (m-30)
REVERT: D   99 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7613 (tm130)
REVERT: D  219 ARG cc_start: 0.1936 (OUTLIER) cc_final: 0.0989 (ttt180)
REVERT: E   66 ASP cc_start: 0.8232 (m-30) cc_final: 0.8010 (m-30)
REVERT: E   99 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7529 (tm130)
REVERT: E  219 ARG cc_start: 0.1892 (OUTLIER) cc_final: 0.0872 (ttt180)
REVERT: F   66 ASP cc_start: 0.8270 (m-30) cc_final: 0.8036 (m-30)
REVERT: F  219 ARG cc_start: 0.2167 (OUTLIER) cc_final: 0.1157 (ttt180)
  outliers start: 23
  outliers final: 8
  residues processed: 179
  average time/residue: 1.4599
  time to fit residues: 278.9048
Evaluate side-chains
  162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0170
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.0220

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.098169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.069356 restraints weight = 20011.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.44
r_work: 0.2849 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10200  Z= 0.123
  Angle     :  0.551   6.857  13896  Z= 0.292
  Chirality :  0.039   0.149   1644
  Planarity :  0.002   0.014   1662
  Dihedral  :  4.027  26.397   1350
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.56 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.63 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.77 (0.24), residues: 1212
  helix:  3.95 (0.15), residues: 882
  sheet:  1.08 (0.52), residues: 60
  loop : -2.72 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 132 
 HIS   0.004   0.001   HIS A 123 
 PHE   0.009   0.001   PHE E  31 
 TYR   0.007   0.001   TYR E 151 
 ARG   0.003   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  751)
  hydrogen bonds       : angle       2.97695 ( 2235)
  SS BOND              : bond        0.00753 (   18)
  SS BOND              : angle       1.55325 (   36)
  covalent geometry    : bond        0.00279 (10182)
  covalent geometry    : angle       0.54564 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 1.161 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8320 (m-30) cc_final: 0.8063 (m-30)
REVERT: A   99 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7575 (tm130)
REVERT: A  219 ARG cc_start: 0.1980 (OUTLIER) cc_final: 0.1045 (ttt180)
REVERT: B   66 ASP cc_start: 0.8256 (m-30) cc_final: 0.8033 (m-30)
REVERT: B   99 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7577 (tm130)
REVERT: B  219 ARG cc_start: 0.1834 (OUTLIER) cc_final: 0.0888 (ttt180)
REVERT: C   66 ASP cc_start: 0.8271 (m-30) cc_final: 0.8015 (m-30)
REVERT: C  219 ARG cc_start: 0.2086 (OUTLIER) cc_final: 0.1147 (ttt180)
REVERT: D   66 ASP cc_start: 0.8324 (m-30) cc_final: 0.8068 (m-30)
REVERT: D   99 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7580 (tm130)
REVERT: D  219 ARG cc_start: 0.1950 (OUTLIER) cc_final: 0.1021 (ttt180)
REVERT: E   66 ASP cc_start: 0.8251 (m-30) cc_final: 0.8014 (m-30)
REVERT: E   99 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7577 (tm130)
REVERT: E  219 ARG cc_start: 0.1853 (OUTLIER) cc_final: 0.0900 (ttt180)
REVERT: F   66 ASP cc_start: 0.8268 (m-30) cc_final: 0.8014 (m-30)
REVERT: F  219 ARG cc_start: 0.2100 (OUTLIER) cc_final: 0.1153 (ttt180)
  outliers start: 20
  outliers final: 10
  residues processed: 174
  average time/residue: 1.6023
  time to fit residues: 297.1415
Evaluate side-chains
  161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN
F  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.094235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.065349 restraints weight = 20223.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.41
r_work: 0.2777 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10200  Z= 0.225
  Angle     :  0.637   9.061  13896  Z= 0.336
  Chirality :  0.043   0.153   1644
  Planarity :  0.003   0.028   1662
  Dihedral  :  4.388  27.332   1350
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  3.30 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.90 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.21 (0.24), residues: 1212
  helix:  3.47 (0.15), residues: 882
  sheet:  1.45 (0.51), residues: 60
  loop : -2.80 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  77 
 HIS   0.004   0.001   HIS B 123 
 PHE   0.010   0.002   PHE F  68 
 TYR   0.013   0.001   TYR E 151 
 ARG   0.003   0.001   ARG E  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04173 (  751)
  hydrogen bonds       : angle       3.19684 ( 2235)
  SS BOND              : bond        0.00911 (   18)
  SS BOND              : angle       2.04284 (   36)
  covalent geometry    : bond        0.00539 (10182)
  covalent geometry    : angle       0.62956 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A   99 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7610 (tm130)
REVERT: B   66 ASP cc_start: 0.8247 (m-30) cc_final: 0.8045 (m-30)
REVERT: B   99 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7552 (tm130)
REVERT: C   66 ASP cc_start: 0.8224 (m-30) cc_final: 0.8002 (m-30)
REVERT: C  153 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8608 (t80)
REVERT: D   99 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7614 (tm130)
REVERT: E   99 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7551 (tm130)
REVERT: F   66 ASP cc_start: 0.8232 (m-30) cc_final: 0.8011 (m-30)
  outliers start: 26
  outliers final: 17
  residues processed: 161
  average time/residue: 1.3092
  time to fit residues: 225.8140
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 2.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 69 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    1.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.095894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.066995 restraints weight = 20292.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.44
r_work: 0.2807 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10200  Z= 0.156
  Angle     :  0.602   8.017  13896  Z= 0.317
  Chirality :  0.040   0.150   1644
  Planarity :  0.002   0.015   1662
  Dihedral  :  4.201  26.736   1350
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.64 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.26 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.38 (0.24), residues: 1212
  helix:  3.63 (0.15), residues: 882
  sheet:  1.31 (0.50), residues: 60
  loop : -2.79 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 132 
 HIS   0.002   0.001   HIS B 123 
 PHE   0.008   0.001   PHE E  68 
 TYR   0.010   0.001   TYR E 151 
 ARG   0.003   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03609 (  751)
  hydrogen bonds       : angle       3.11226 ( 2235)
  SS BOND              : bond        0.00809 (   18)
  SS BOND              : angle       1.78312 (   36)
  covalent geometry    : bond        0.00370 (10182)
  covalent geometry    : angle       0.59573 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7551 (tm130)
REVERT: A  219 ARG cc_start: 0.1976 (OUTLIER) cc_final: 0.0931 (ttt180)
REVERT: B   66 ASP cc_start: 0.8240 (m-30) cc_final: 0.8011 (m-30)
REVERT: B   99 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7532 (tm-30)
REVERT: B  219 ARG cc_start: 0.1903 (OUTLIER) cc_final: 0.0861 (ttt180)
REVERT: C   66 ASP cc_start: 0.8223 (m-30) cc_final: 0.7960 (m-30)
REVERT: C  219 ARG cc_start: 0.2042 (OUTLIER) cc_final: 0.1029 (ttt180)
REVERT: D   99 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7508 (tm130)
REVERT: D  219 ARG cc_start: 0.1964 (OUTLIER) cc_final: 0.0931 (ttt180)
REVERT: E   66 ASP cc_start: 0.8140 (m-30) cc_final: 0.7927 (m-30)
REVERT: E   99 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: E  219 ARG cc_start: 0.1985 (OUTLIER) cc_final: 0.0941 (ttt180)
REVERT: F   66 ASP cc_start: 0.8229 (m-30) cc_final: 0.7963 (m-30)
REVERT: F  219 ARG cc_start: 0.2023 (OUTLIER) cc_final: 0.1001 (ttt180)
  outliers start: 26
  outliers final: 20
  residues processed: 171
  average time/residue: 1.5969
  time to fit residues: 291.3433
Evaluate side-chains
  167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  146 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 70 optimal weight:   20.0000
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 99 optimal weight:    0.7980
   chunk 30 optimal weight:   30.0000
   chunk 89 optimal weight:    7.9990
   overall best weight:    2.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.094066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.065154 restraints weight = 20206.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.42
r_work: 0.2782 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10200  Z= 0.212
  Angle     :  0.649   8.914  13896  Z= 0.340
  Chirality :  0.042   0.153   1644
  Planarity :  0.003   0.026   1662
  Dihedral  :  4.365  26.629   1350
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  3.14 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.99 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.15 (0.24), residues: 1212
  helix:  3.40 (0.15), residues: 882
  sheet:  1.62 (0.54), residues: 60
  loop : -2.77 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  77 
 HIS   0.002   0.001   HIS D 100 
 PHE   0.010   0.002   PHE C  68 
 TYR   0.013   0.002   TYR E 151 
 ARG   0.003   0.000   ARG E  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  751)
  hydrogen bonds       : angle       3.22000 ( 2235)
  SS BOND              : bond        0.00887 (   18)
  SS BOND              : angle       2.05844 (   36)
  covalent geometry    : bond        0.00507 (10182)
  covalent geometry    : angle       0.64131 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 146
  time to evaluate  : 1.194 
Fit side-chains
REVERT: A   99 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: A  219 ARG cc_start: 0.2094 (OUTLIER) cc_final: 0.0899 (ttt180)
REVERT: B   66 ASP cc_start: 0.8248 (m-30) cc_final: 0.8046 (m-30)
REVERT: B   99 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: B  219 ARG cc_start: 0.2027 (OUTLIER) cc_final: 0.0854 (ttt180)
REVERT: C   66 ASP cc_start: 0.8232 (m-30) cc_final: 0.8001 (m-30)
REVERT: C  219 ARG cc_start: 0.2105 (OUTLIER) cc_final: 0.0959 (ttt180)
REVERT: D   99 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7599 (tm-30)
REVERT: D  219 ARG cc_start: 0.2086 (OUTLIER) cc_final: 0.0898 (ttt180)
REVERT: E   66 ASP cc_start: 0.8185 (m-30) cc_final: 0.7979 (m-30)
REVERT: E   99 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: E  219 ARG cc_start: 0.2037 (OUTLIER) cc_final: 0.0867 (ttt180)
REVERT: F   66 ASP cc_start: 0.8234 (m-30) cc_final: 0.8004 (m-30)
REVERT: F  219 ARG cc_start: 0.2084 (OUTLIER) cc_final: 0.0956 (ttt180)
  outliers start: 40
  outliers final: 26
  residues processed: 181
  average time/residue: 1.3462
  time to fit residues: 259.5584
Evaluate side-chains
  172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  146 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 114 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 101 optimal weight:    8.9990
   chunk 106 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    0.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.098264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.069482 restraints weight = 19950.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.46
r_work: 0.2861 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10200  Z= 0.125
  Angle     :  0.617   7.850  13896  Z= 0.323
  Chirality :  0.040   0.146   1644
  Planarity :  0.003   0.021   1662
  Dihedral  :  4.099  25.809   1350
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.81 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.16 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.65 (0.24), residues: 1212
  helix:  3.82 (0.15), residues: 882
  sheet:  1.40 (0.59), residues: 60
  loop : -2.69 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 132 
 HIS   0.002   0.000   HIS D  97 
 PHE   0.009   0.001   PHE E  31 
 TYR   0.012   0.001   TYR E 211 
 ARG   0.004   0.000   ARG E 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 (  751)
  hydrogen bonds       : angle       3.07711 ( 2235)
  SS BOND              : bond        0.00699 (   18)
  SS BOND              : angle       1.45460 (   36)
  covalent geometry    : bond        0.00280 (10182)
  covalent geometry    : angle       0.61366 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 1.161 
Fit side-chains
REVERT: A  219 ARG cc_start: 0.1977 (OUTLIER) cc_final: 0.0984 (ttt180)
REVERT: B   66 ASP cc_start: 0.8291 (m-30) cc_final: 0.8034 (m-30)
REVERT: B   99 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: B  208 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8786 (mm-30)
REVERT: B  219 ARG cc_start: 0.1956 (OUTLIER) cc_final: 0.0983 (ttt180)
REVERT: C   66 ASP cc_start: 0.8263 (m-30) cc_final: 0.7972 (m-30)
REVERT: C  219 ARG cc_start: 0.2076 (OUTLIER) cc_final: 0.1091 (ttt180)
REVERT: D  219 ARG cc_start: 0.1971 (OUTLIER) cc_final: 0.0980 (ttt180)
REVERT: E   66 ASP cc_start: 0.8176 (m-30) cc_final: 0.7927 (m-30)
REVERT: E   99 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: E  208 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8790 (mm-30)
REVERT: E  219 ARG cc_start: 0.2014 (OUTLIER) cc_final: 0.0990 (ttt180)
REVERT: F   66 ASP cc_start: 0.8263 (m-30) cc_final: 0.7970 (m-30)
REVERT: F  219 ARG cc_start: 0.2083 (OUTLIER) cc_final: 0.1096 (ttt180)
  outliers start: 30
  outliers final: 18
  residues processed: 184
  average time/residue: 1.2811
  time to fit residues: 251.3915
Evaluate side-chains
  164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  208 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 100 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  99 GLN
F  99 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.096756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.068001 restraints weight = 20257.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.46
r_work: 0.2842 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10200  Z= 0.157
  Angle     :  0.652   8.292  13896  Z= 0.341
  Chirality :  0.041   0.163   1644
  Planarity :  0.003   0.021   1662
  Dihedral  :  4.187  25.533   1350
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  2.97 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.79 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (0.24), residues: 1212
  helix:  3.71 (0.15), residues: 882
  sheet:  1.67 (0.63), residues: 60
  loop : -2.54 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  44 
 HIS   0.001   0.001   HIS B 123 
 PHE   0.009   0.001   PHE B  31 
 TYR   0.015   0.001   TYR E 211 
 ARG   0.003   0.000   ARG F  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  751)
  hydrogen bonds       : angle       3.16694 ( 2235)
  SS BOND              : bond        0.00729 (   18)
  SS BOND              : angle       1.68732 (   36)
  covalent geometry    : bond        0.00369 (10182)
  covalent geometry    : angle       0.64729 (13860)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.147 
Fit side-chains
REVERT: A  219 ARG cc_start: 0.2083 (OUTLIER) cc_final: 0.1051 (ttt180)
REVERT: B   66 ASP cc_start: 0.8298 (m-30) cc_final: 0.8073 (m-30)
REVERT: B   99 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: B  208 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8790 (mm-30)
REVERT: B  219 ARG cc_start: 0.2165 (OUTLIER) cc_final: 0.1133 (ttt180)
REVERT: C   66 ASP cc_start: 0.8225 (m-30) cc_final: 0.7988 (m-30)
REVERT: C  219 ARG cc_start: 0.2079 (OUTLIER) cc_final: 0.1041 (ttt180)
REVERT: D  219 ARG cc_start: 0.2072 (OUTLIER) cc_final: 0.1047 (ttt180)
REVERT: E   66 ASP cc_start: 0.8208 (m-30) cc_final: 0.7979 (m-30)
REVERT: E   99 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7491 (tm-30)
REVERT: E  208 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8771 (mm-30)
REVERT: E  219 ARG cc_start: 0.2143 (OUTLIER) cc_final: 0.1087 (ttt180)
REVERT: F   66 ASP cc_start: 0.8210 (m-30) cc_final: 0.7976 (m-30)
REVERT: F  219 ARG cc_start: 0.2062 (OUTLIER) cc_final: 0.1028 (ttt180)
  outliers start: 33
  outliers final: 19
  residues processed: 171
  average time/residue: 1.6509
  time to fit residues: 299.9470
Evaluate side-chains
  160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  208 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 5 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 60 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.096915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.068046 restraints weight = 19984.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.45
r_work: 0.2842 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10200  Z= 0.155
  Angle     :  0.658   8.186  13896  Z= 0.344
  Chirality :  0.041   0.150   1644
  Planarity :  0.003   0.024   1662
  Dihedral  :  4.180  25.482   1350
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  3.14 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.79 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.61 (0.24), residues: 1212
  helix:  3.71 (0.16), residues: 882
  sheet:  1.75 (0.63), residues: 60
  loop : -2.45 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 132 
 HIS   0.002   0.001   HIS F  94 
 PHE   0.009   0.001   PHE B  31 
 TYR   0.017   0.001   TYR E 211 
 ARG   0.003   0.000   ARG E 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  751)
  hydrogen bonds       : angle       3.24505 ( 2235)
  SS BOND              : bond        0.00744 (   18)
  SS BOND              : angle       1.70401 (   36)
  covalent geometry    : bond        0.00365 (10182)
  covalent geometry    : angle       0.65282 (13860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7557.82 seconds
wall clock time: 135 minutes 5.82 seconds (8105.82 seconds total)