Starting phenix.real_space_refine
on Tue Mar  3 12:16:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wfq_21652/03_2026/6wfq_21652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wfq_21652/03_2026/6wfq_21652.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2026/6wfq_21652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2026/6wfq_21652.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2026/6wfq_21652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2026/6wfq_21652.cif"
  }
  resolution = 3.9
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      30      5.49       5
     S      10      5.16       5
     C    2508      2.51       5
     N     769      2.21       5
     O     847      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4164
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1812
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 9, 'TRANS': 218}
    Chain: "D"
      Number of atoms: 1737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1737
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 8, 'TRANS': 210}
    Chain: "A"
      Number of atoms: 313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 313
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "B"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 302
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
  Time building chain proxies: 1.15, per 1000 atoms: 0.28
  Number of scatterers: 4164
  At special positions: 0
  Unit cell: (80.24, 99.96, 82.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P      30     15.00
     O     847      8.00
     N     769      7.00
     C    2508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 149.2 milliseconds
  

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  854

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      75.2% alpha, 0.0% beta
      13 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'C' and resid 31 through 46
      removed outlier: 4.013A  pdb=" N   MET C  35 " --> pdb=" O   LYS C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 66
    Processing helix  chain 'C' and resid 68 through 83
      removed outlier: 3.714A  pdb=" N   VAL C  72 " --> pdb=" O   GLY C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 107
      removed outlier: 3.585A  pdb=" N   ILE C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 117
      removed outlier: 3.691A  pdb=" N   PHE C 114 " --> pdb=" O   MET C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 142
    Processing helix  chain 'C' and resid 146 through 158
      removed outlier: 4.130A  pdb=" N   LEU C 150 " --> pdb=" O   GLU C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 181
      removed outlier: 4.326A  pdb=" N   ILE C 169 " --> pdb=" O   ASN C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 201
    Processing helix  chain 'C' and resid 210 through 232
    Processing helix  chain 'C' and resid 233 through 248
      removed outlier: 3.782A  pdb=" N   ALA C 237 " --> pdb=" O   ASP C 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 3.956A  pdb=" N   MET D  35 " --> pdb=" O   LYS D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 66
    Processing helix  chain 'D' and resid 68 through 83
      removed outlier: 3.671A  pdb=" N   VAL D  72 " --> pdb=" O   GLY D  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 111
      removed outlier: 3.795A  pdb=" N   ILE D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 133
      removed outlier: 3.785A  pdb=" N   HIS D 123 " --> pdb=" O   GLY D 119 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE D 124 " --> pdb=" O   GLY D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 143
      removed outlier: 3.984A  pdb=" N   HIS D 142 " --> pdb=" O   TYR D 138 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 161
      removed outlier: 3.996A  pdb=" N   LEU D 150 " --> pdb=" O   GLU D 146 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE D 157 " --> pdb=" O   LYS D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 181
    Processing helix  chain 'D' and resid 185 through 203
    Processing helix  chain 'D' and resid 208 through 231
      removed outlier: 3.621A  pdb=" N   GLU D 213 " --> pdb=" O   GLN D 209 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA D 224 " --> pdb=" O   GLN D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 248
      removed outlier: 3.803A  pdb=" N   ALA D 237 " --> pdb=" O   ASP D 233 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL D 248 " --> pdb=" O   HIS D 244 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    687 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      30 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 0.65

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1063
        1.33 -     1.45: 878
        1.45 -     1.57: 2281
        1.57 -     1.69: 58
        1.69 -     1.80: 20
  Bond restraints: 4300
  Sorted by residual:
  bond pdb=" CB  PRO D 204 "
       pdb=" CG  PRO D 204 "
    ideal  model  delta    sigma   weight residual
    1.492  1.536 -0.044 5.00e-02 4.00e+02 7.61e-01
  bond pdb=" CA  LYS C  31 "
       pdb=" C   LYS C  31 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.34e-02 5.57e+03 5.46e-01
  bond pdb=" C2'  DT A   3 "
       pdb=" C1'  DT A   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.537 -0.012 2.00e-02 2.50e+03 3.75e-01
  bond pdb=" C   ARG D  97 "
       pdb=" N   PRO D  98 "
    ideal  model  delta    sigma   weight residual
    1.331  1.338 -0.008 1.31e-02 5.83e+03 3.38e-01
  bond pdb=" C   ILE C 182 "
       pdb=" N   PRO C 183 "
    ideal  model  delta    sigma   weight residual
    1.335  1.343 -0.007 1.30e-02 5.92e+03 3.33e-01
  ... (remaining 4295 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 5762
        1.27 -     2.54: 141
        2.54 -     3.81: 22
        3.81 -     5.08: 7
        5.08 -     6.35: 3
  Bond angle restraints: 5935
  Sorted by residual:
  angle pdb=" N   LYS D 112 "
        pdb=" CA  LYS D 112 "
        pdb=" C   LYS D 112 "
      ideal   model   delta    sigma   weight residual
     114.62  110.96    3.66 1.14e+00 7.69e-01 1.03e+01
  angle pdb=" CA  LYS D 112 "
        pdb=" C   LYS D 112 "
        pdb=" N   ASP D 113 "
      ideal   model   delta    sigma   weight residual
     119.71  116.95    2.76 1.17e+00 7.31e-01 5.57e+00
  angle pdb=" N   LYS C  82 "
        pdb=" CA  LYS C  82 "
        pdb=" C   LYS C  82 "
      ideal   model   delta    sigma   weight residual
     112.54  109.84    2.70 1.22e+00 6.72e-01 4.90e+00
  angle pdb=" N   SER D  33 "
        pdb=" CA  SER D  33 "
        pdb=" C   SER D  33 "
      ideal   model   delta    sigma   weight residual
     111.37  114.89   -3.52 1.65e+00 3.67e-01 4.55e+00
  angle pdb=" O   HIS C 244 "
        pdb=" C   HIS C 244 "
        pdb=" N   LEU C 245 "
      ideal   model   delta    sigma   weight residual
     122.15  119.88    2.27 1.14e+00 7.69e-01 3.97e+00
  ... (remaining 5930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 2176
       16.59 -    33.17: 233
       33.17 -    49.76: 106
       49.76 -    66.34: 37
       66.34 -    82.93: 2
  Dihedral angle restraints: 2554
    sinusoidal: 1251
      harmonic: 1303
  Sorted by residual:
  dihedral pdb=" N   LEU C  79 "
           pdb=" CA  LEU C  79 "
           pdb=" CB  LEU C  79 "
           pdb=" CG  LEU C  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.66   59.66     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LYS C  82 "
           pdb=" CB  LYS C  82 "
           pdb=" CG  LYS C  82 "
           pdb=" CD  LYS C  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.92   58.08     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CB  LYS C  82 "
           pdb=" CG  LYS C  82 "
           pdb=" CD  LYS C  82 "
           pdb=" CE  LYS C  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -2.32  -57.68     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 2551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 402
       0.023 -    0.045: 161
       0.045 -    0.068: 68
       0.068 -    0.090: 16
       0.090 -    0.113: 12
  Chirality restraints: 659
  Sorted by residual:
  chirality pdb=" CA  ILE D  87 "
            pdb=" N   ILE D  87 "
            pdb=" C   ILE D  87 "
            pdb=" CB  ILE D  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.17e-01
  chirality pdb=" CA  ILE C  87 "
            pdb=" N   ILE C  87 "
            pdb=" C   ILE C  87 "
            pdb=" CB  ILE C  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.87e-01
  chirality pdb=" CA  PRO C 118 "
            pdb=" N   PRO C 118 "
            pdb=" C   PRO C 118 "
            pdb=" CB  PRO C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.76e-01
  ... (remaining 656 not shown)

  Planarity restraints: 686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C 244 "   -0.023 2.00e-02 2.50e+03   4.55e-02 2.07e+01
        pdb=" C   HIS C 244 "    0.079 2.00e-02 2.50e+03
        pdb=" O   HIS C 244 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   LEU C 245 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D 244 "   -0.019 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   HIS D 244 "    0.065 2.00e-02 2.50e+03
        pdb=" O   HIS D 244 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU D 245 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C  69 "   -0.014 5.00e-02 4.00e+02   2.08e-02 6.92e-01
        pdb=" N   PRO C  70 "    0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO C  70 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO C  70 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 683 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 941
        2.79 -     3.32: 4114
        3.32 -     3.85: 7107
        3.85 -     4.37: 7847
        4.37 -     4.90: 12239
  Nonbonded interactions: 32248
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 131 "
            pdb=" OG  SER D 134 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LEU D 211 "
            pdb=" ND2 ASN D 215 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" O   SER C  99 "
            pdb=" OG1 THR C 102 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   ASN D 158 "
            pdb=" OG  SER D 161 "
     model   vdw
     2.399 3.040
  nonbonded pdb=" O   GLU C 156 "
            pdb=" OG  SER C 159 "
     model   vdw
     2.399 3.040
  ... (remaining 32243 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
Found NCS groups:
ncs_group {
  reference = (chain 'C' and resid 30 through 248)
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.030
  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:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.030
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4300  Z= 0.110
  Angle     :  0.487   6.347   5935  Z= 0.295
  Chirality :  0.032   0.113    659
  Planarity :  0.003   0.045    686
  Dihedral  : 16.898  82.929   1700
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.32 %
    Favored  : 93.88 %
  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: -2.49 (0.35), residues: 443
  helix: -0.75 (0.26), residues: 316
  sheet:  None (None), residues: 0
  loop : -3.85 (0.44), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  46 
 TYR   0.014   0.001   TYR D 219 
 PHE   0.003   0.000   PHE C 131 
 TRP   0.001   0.000   TRP D 198 
 HIS   0.004   0.000   HIS C 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 4300)
  covalent geometry    : angle       0.48749 ( 5935)
  hydrogen bonds       : bond        0.15908 (  259)
  hydrogen bonds       : angle       5.18924 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  126 GLN cc_start: 0.9374 (tt0) cc_final: 0.8509 (tp40)
REVERT: C  130 PHE cc_start: 0.9371 (m-10) cc_final: 0.8486 (m-80)
REVERT: C  138 TYR cc_start: 0.8711 (t80) cc_final: 0.8335 (t80)
REVERT: C  153 LYS cc_start: 0.9737 (pptt) cc_final: 0.9444 (tppt)
REVERT: C  157 ILE cc_start: 0.9453 (tp) cc_final: 0.9055 (tp)
REVERT: C  196 LEU cc_start: 0.9633 (mm) cc_final: 0.9379 (pp)
REVERT: C  212 HIS cc_start: 0.9478 (p-80) cc_final: 0.9228 (m-70)
REVERT: D   89 ASN cc_start: 0.8707 (t0) cc_final: 0.8426 (m-40)
REVERT: D  135 LEU cc_start: 0.8854 (mt) cc_final: 0.8618 (mt)
REVERT: D  147 GLN cc_start: 0.9042 (mp10) cc_final: 0.8619 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0745
  time to fit residues: 11.2734
Evaluate side-chains
  74 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:   30.0000
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.6582

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

Flipped N/Q/H residues before XYZ refinement:
C  42 GLN
D 192 HIS
D 214 HIS
D 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.068489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.047721 restraints weight = 21360.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.049376 restraints weight = 14483.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.050584 restraints weight = 11182.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.051457 restraints weight = 9328.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.052089 restraints weight = 8185.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4300  Z= 0.136
  Angle     :  0.662  10.461   5935  Z= 0.336
  Chirality :  0.038   0.180    659
  Planarity :  0.004   0.027    686
  Dihedral  : 18.339  59.771    822
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.43 %
    Favored  : 83.24 %
  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: -0.80 (0.39), residues: 443
  helix:  0.55 (0.28), residues: 320
  sheet:  None (None), residues: 0
  loop : -3.48 (0.45), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.022   0.003   TYR C 219 
 PHE   0.010   0.001   PHE D  65 
 TRP   0.002   0.001   TRP C 198 
 HIS   0.004   0.001   HIS C 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4300)
  covalent geometry    : angle       0.66200 ( 5935)
  hydrogen bonds       : bond        0.03482 (  259)
  hydrogen bonds       : angle       3.83782 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 GLN cc_start: 0.8859 (pt0) cc_final: 0.8366 (pt0)
REVERT: C  126 GLN cc_start: 0.9471 (tt0) cc_final: 0.8607 (tp40)
REVERT: C  130 PHE cc_start: 0.9388 (m-10) cc_final: 0.8585 (m-80)
REVERT: C  138 TYR cc_start: 0.8795 (t80) cc_final: 0.8275 (t80)
REVERT: C  153 LYS cc_start: 0.9741 (pptt) cc_final: 0.9495 (tptt)
REVERT: C  212 HIS cc_start: 0.9399 (p-80) cc_final: 0.9193 (m-70)
REVERT: D   35 MET cc_start: 0.9583 (tmm) cc_final: 0.9299 (ppp)
REVERT: D   89 ASN cc_start: 0.8762 (t0) cc_final: 0.8535 (m-40)
REVERT: D   97 ARG cc_start: 0.8914 (mmp80) cc_final: 0.8230 (mmp80)
REVERT: D  147 GLN cc_start: 0.8966 (mp10) cc_final: 0.8582 (mp10)
  outliers start: 5
  outliers final: 2
  residues processed: 83
  average time/residue: 0.0770
  time to fit residues: 7.9669
Evaluate side-chains
  81 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   76 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
D 192 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.067210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.046962 restraints weight = 21038.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.048554 restraints weight = 14210.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.049731 restraints weight = 10954.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050564 restraints weight = 9099.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.051141 restraints weight = 7960.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4300  Z= 0.143
  Angle     :  0.665   9.792   5935  Z= 0.339
  Chirality :  0.038   0.136    659
  Planarity :  0.004   0.036    686
  Dihedral  : 18.400  59.939    822
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.02 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.39), residues: 443
  helix:  0.66 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop : -3.32 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.015   0.002   TYR D 219 
 PHE   0.015   0.001   PHE D 114 
 TRP   0.002   0.001   TRP C 198 
 HIS   0.004   0.001   HIS D 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4300)
  covalent geometry    : angle       0.66494 ( 5935)
  hydrogen bonds       : bond        0.03545 (  259)
  hydrogen bonds       : angle       3.83189 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 GLN cc_start: 0.8852 (pt0) cc_final: 0.8631 (pt0)
REVERT: C   43 MET cc_start: 0.9279 (mmm) cc_final: 0.9041 (mmm)
REVERT: C   62 MET cc_start: 0.8609 (ttp) cc_final: 0.8183 (mtp)
REVERT: C  126 GLN cc_start: 0.9469 (tt0) cc_final: 0.8702 (tp40)
REVERT: C  130 PHE cc_start: 0.9479 (m-10) cc_final: 0.8734 (m-80)
REVERT: C  153 LYS cc_start: 0.9736 (pptt) cc_final: 0.9466 (tptt)
REVERT: C  157 ILE cc_start: 0.9443 (tp) cc_final: 0.9072 (tp)
REVERT: C  181 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8776 (mt-10)
REVERT: C  212 HIS cc_start: 0.9392 (p-80) cc_final: 0.9141 (m-70)
REVERT: D   42 GLN cc_start: 0.9517 (tp-100) cc_final: 0.9259 (tm-30)
REVERT: D   43 MET cc_start: 0.9481 (mmt) cc_final: 0.9055 (mmt)
REVERT: D   62 MET cc_start: 0.1734 (ttt) cc_final: 0.1199 (tpp)
REVERT: D   97 ARG cc_start: 0.8976 (mmp80) cc_final: 0.8322 (mmp80)
REVERT: D  110 MET cc_start: 0.8191 (tpt) cc_final: 0.7748 (tpt)
REVERT: D  147 GLN cc_start: 0.8961 (mp10) cc_final: 0.8553 (mp10)
REVERT: D  221 GLN cc_start: 0.9052 (mt0) cc_final: 0.8617 (mt0)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0743
  time to fit residues: 7.7226
Evaluate side-chains
  80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
C  42 GLN
C 215 ASN
C 242 GLN
D 126 GLN
** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.065871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.045785 restraints weight = 21055.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.047392 restraints weight = 14057.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.048564 restraints weight = 10741.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.049391 restraints weight = 8897.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.049995 restraints weight = 7769.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4300  Z= 0.146
  Angle     :  0.673   9.944   5935  Z= 0.343
  Chirality :  0.041   0.335    659
  Planarity :  0.004   0.033    686
  Dihedral  : 18.572  59.999    822
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.49 %
    Favored  : 80.05 %
  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: -0.27 (0.39), residues: 443
  helix:  0.86 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -3.18 (0.49), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.013   0.002   TYR D 219 
 PHE   0.012   0.001   PHE D 175 
 TRP   0.002   0.001   TRP D 198 
 HIS   0.007   0.001   HIS D 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4300)
  covalent geometry    : angle       0.67306 ( 5935)
  hydrogen bonds       : bond        0.03491 (  259)
  hydrogen bonds       : angle       3.84402 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.9525 (tmm) cc_final: 0.9120 (ppp)
REVERT: C   42 GLN cc_start: 0.8908 (pt0) cc_final: 0.8624 (pt0)
REVERT: C   43 MET cc_start: 0.9370 (mmm) cc_final: 0.9099 (mmm)
REVERT: C   62 MET cc_start: 0.8663 (ttp) cc_final: 0.8345 (mtp)
REVERT: C  126 GLN cc_start: 0.9454 (tt0) cc_final: 0.8726 (tp40)
REVERT: C  130 PHE cc_start: 0.9479 (m-10) cc_final: 0.8817 (m-80)
REVERT: C  181 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8728 (mt-10)
REVERT: C  212 HIS cc_start: 0.9401 (p-80) cc_final: 0.9117 (m-70)
REVERT: D   89 ASN cc_start: 0.8202 (m-40) cc_final: 0.7996 (m-40)
REVERT: D  110 MET cc_start: 0.8089 (tpt) cc_final: 0.7664 (tpt)
REVERT: D  147 GLN cc_start: 0.8983 (mp10) cc_final: 0.8575 (mp10)
REVERT: D  188 PHE cc_start: 0.9474 (m-80) cc_final: 0.9159 (m-80)
REVERT: D  221 GLN cc_start: 0.9041 (mt0) cc_final: 0.8832 (mp10)
  outliers start: 13
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0748
  time to fit residues: 7.8361
Evaluate side-chains
  84 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  117 HIS
Chi-restraints excluded: chain D residue  170 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0000
   chunk 1 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.8188

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

Flipped N/Q/H residues before XYZ refinement:
** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.067870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.047464 restraints weight = 20672.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.049134 restraints weight = 13793.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050368 restraints weight = 10508.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.051243 restraints weight = 8677.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.051874 restraints weight = 7567.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4300  Z= 0.127
  Angle     :  0.709  13.241   5935  Z= 0.348
  Chirality :  0.039   0.147    659
  Planarity :  0.003   0.028    686
  Dihedral  : 18.587  59.242    822
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.95 %
    Favored  : 77.93 %
  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: -0.14 (0.40), residues: 443
  helix:  0.88 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -2.94 (0.50), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  94 
 TYR   0.013   0.002   TYR D 219 
 PHE   0.012   0.001   PHE D 175 
 TRP   0.002   0.001   TRP D 198 
 HIS   0.013   0.001   HIS D 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4300)
  covalent geometry    : angle       0.70929 ( 5935)
  hydrogen bonds       : bond        0.03230 (  259)
  hydrogen bonds       : angle       3.71957 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 GLU cc_start: 0.9575 (pp20) cc_final: 0.9318 (pp20)
REVERT: C   42 GLN cc_start: 0.8904 (pt0) cc_final: 0.8585 (pt0)
REVERT: C   43 MET cc_start: 0.9412 (mmm) cc_final: 0.9110 (mmm)
REVERT: C  126 GLN cc_start: 0.9425 (tt0) cc_final: 0.8664 (tp40)
REVERT: C  130 PHE cc_start: 0.9459 (m-10) cc_final: 0.8711 (m-80)
REVERT: C  181 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8705 (mt-10)
REVERT: C  212 HIS cc_start: 0.9383 (p-80) cc_final: 0.9102 (m-70)
REVERT: D   42 GLN cc_start: 0.9507 (tp-100) cc_final: 0.9272 (tm-30)
REVERT: D   43 MET cc_start: 0.9519 (mmt) cc_final: 0.9097 (mmt)
REVERT: D   62 MET cc_start: 0.1212 (ttt) cc_final: 0.0904 (tpp)
REVERT: D   97 ARG cc_start: 0.8823 (mmp80) cc_final: 0.8144 (mmp80)
REVERT: D  110 MET cc_start: 0.7846 (tpt) cc_final: 0.7427 (tpt)
REVERT: D  131 PHE cc_start: 0.7655 (t80) cc_final: 0.7422 (t80)
REVERT: D  147 GLN cc_start: 0.8890 (mp10) cc_final: 0.8479 (mp10)
REVERT: D  188 PHE cc_start: 0.9451 (m-80) cc_final: 0.9083 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0769
  time to fit residues: 8.3155
Evaluate side-chains
  80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  117 HIS
Chi-restraints excluded: chain D residue  170 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:   40.0000
   chunk 18 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.063981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.043946 restraints weight = 21595.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.045432 restraints weight = 14683.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.046501 restraints weight = 11345.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.047301 restraints weight = 9487.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.047861 restraints weight = 8326.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4300  Z= 0.205
  Angle     :  0.773  12.606   5935  Z= 0.398
  Chirality :  0.042   0.215    659
  Planarity :  0.004   0.035    686
  Dihedral  : 18.966  59.296    822
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.54 %
    Favored  : 75.53 %
  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: -0.30 (0.39), residues: 443
  helix:  0.70 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -2.72 (0.54), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  97 
 TYR   0.012   0.003   TYR D 138 
 PHE   0.013   0.001   PHE D 175 
 TRP   0.011   0.002   TRP D 198 
 HIS   0.008   0.002   HIS D 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4300)
  covalent geometry    : angle       0.77297 ( 5935)
  hydrogen bonds       : bond        0.04627 (  259)
  hydrogen bonds       : angle       4.23794 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.9557 (tmm) cc_final: 0.9188 (ppp)
REVERT: C   42 GLN cc_start: 0.8891 (pt0) cc_final: 0.8547 (pt0)
REVERT: C   43 MET cc_start: 0.9406 (mmm) cc_final: 0.9121 (mmm)
REVERT: C  126 GLN cc_start: 0.9468 (tt0) cc_final: 0.8790 (tp40)
REVERT: C  130 PHE cc_start: 0.9506 (m-10) cc_final: 0.9020 (m-80)
REVERT: C  138 TYR cc_start: 0.8978 (t80) cc_final: 0.8558 (t80)
REVERT: C  181 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8828 (mt-10)
REVERT: D   62 MET cc_start: 0.1917 (ttt) cc_final: 0.1629 (tpp)
REVERT: D  110 MET cc_start: 0.8123 (tpt) cc_final: 0.7585 (tpt)
REVERT: D  147 GLN cc_start: 0.9001 (mp10) cc_final: 0.8606 (mp10)
  outliers start: 11
  outliers final: 8
  residues processed: 76
  average time/residue: 0.0651
  time to fit residues: 6.3411
Evaluate side-chains
  75 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  219 TYR
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  117 HIS
Chi-restraints excluded: chain D residue  170 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 6 optimal weight:    0.0020
   chunk 41 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.066863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.046569 restraints weight = 20218.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.048159 restraints weight = 13513.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.049338 restraints weight = 10352.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050168 restraints weight = 8559.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.050808 restraints weight = 7463.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4300  Z= 0.134
  Angle     :  0.768  11.117   5935  Z= 0.379
  Chirality :  0.041   0.162    659
  Planarity :  0.003   0.027    686
  Dihedral  : 18.982  59.697    822
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 24.47 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.40), residues: 443
  helix:  0.81 (0.29), residues: 328
  sheet:  None (None), residues: 0
  loop : -2.78 (0.51), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.014   0.002   TYR D 219 
 PHE   0.035   0.001   PHE D 175 
 TRP   0.007   0.001   TRP D 198 
 HIS   0.004   0.001   HIS C 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4300)
  covalent geometry    : angle       0.76825 ( 5935)
  hydrogen bonds       : bond        0.03555 (  259)
  hydrogen bonds       : angle       4.02465 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   34 GLU cc_start: 0.9499 (mp0) cc_final: 0.9239 (mp0)
REVERT: C   35 MET cc_start: 0.9549 (tmm) cc_final: 0.9109 (ppp)
REVERT: C   37 GLU cc_start: 0.9590 (pp20) cc_final: 0.9385 (pp20)
REVERT: C   42 GLN cc_start: 0.8952 (pt0) cc_final: 0.8610 (pt0)
REVERT: C   43 MET cc_start: 0.9441 (mmm) cc_final: 0.9140 (mmm)
REVERT: C   62 MET cc_start: 0.8314 (mtm) cc_final: 0.7984 (mtt)
REVERT: C  126 GLN cc_start: 0.9416 (tt0) cc_final: 0.8699 (tp40)
REVERT: C  130 PHE cc_start: 0.9483 (m-10) cc_final: 0.8790 (m-80)
REVERT: C  138 TYR cc_start: 0.8872 (t80) cc_final: 0.8486 (t80)
REVERT: C  149 ASP cc_start: 0.9584 (m-30) cc_final: 0.9311 (p0)
REVERT: C  181 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8775 (mt-10)
REVERT: D  110 MET cc_start: 0.7819 (tpt) cc_final: 0.7376 (tpt)
REVERT: D  147 GLN cc_start: 0.8939 (mp10) cc_final: 0.8530 (mp10)
REVERT: D  181 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8788 (mt-10)
REVERT: D  221 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8976 (pp30)
  outliers start: 8
  outliers final: 7
  residues processed: 82
  average time/residue: 0.0675
  time to fit residues: 7.0522
Evaluate side-chains
  80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  117 HIS
Chi-restraints excluded: chain D residue  192 HIS
Chi-restraints excluded: chain D residue  221 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 35 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    0.1980
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 216 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.064526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.044652 restraints weight = 20590.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.046139 restraints weight = 14060.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.047238 restraints weight = 10885.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.048034 restraints weight = 9071.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.048589 restraints weight = 7952.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.4495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   4300  Z= 0.174
  Angle     :  0.802  16.479   5935  Z= 0.407
  Chirality :  0.041   0.191    659
  Planarity :  0.004   0.027    686
  Dihedral  : 18.976  58.475    822
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.20 %
    Favored  : 72.61 %
  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: -0.29 (0.40), residues: 443
  helix:  0.66 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.61 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.012   0.003   TYR D 219 
 PHE   0.024   0.001   PHE D 175 
 TRP   0.003   0.001   TRP C 198 
 HIS   0.005   0.001   HIS C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4300)
  covalent geometry    : angle       0.80225 ( 5935)
  hydrogen bonds       : bond        0.04186 (  259)
  hydrogen bonds       : angle       4.31609 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.9569 (tmm) cc_final: 0.9158 (ppp)
REVERT: C   37 GLU cc_start: 0.9633 (pp20) cc_final: 0.9415 (pp20)
REVERT: C   43 MET cc_start: 0.9430 (mmm) cc_final: 0.9136 (tpp)
REVERT: C   62 MET cc_start: 0.8308 (mtm) cc_final: 0.7988 (mtt)
REVERT: C  126 GLN cc_start: 0.9420 (tt0) cc_final: 0.8770 (tp-100)
REVERT: C  130 PHE cc_start: 0.9499 (m-10) cc_final: 0.9021 (m-80)
REVERT: C  138 TYR cc_start: 0.8966 (t80) cc_final: 0.8504 (t80)
REVERT: C  149 ASP cc_start: 0.9606 (m-30) cc_final: 0.9343 (p0)
REVERT: C  181 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8819 (mt-10)
REVERT: D  110 MET cc_start: 0.8050 (tpt) cc_final: 0.7620 (tpt)
REVERT: D  147 GLN cc_start: 0.9002 (mp10) cc_final: 0.8601 (mp10)
  outliers start: 12
  outliers final: 10
  residues processed: 77
  average time/residue: 0.0610
  time to fit residues: 6.0513
Evaluate side-chains
  78 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  117 HIS
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  198 TRP
Chi-restraints excluded: chain D residue  221 GLN
Chi-restraints excluded: chain D residue  226 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0020
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
C 117 HIS
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.065446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.045236 restraints weight = 20843.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.046812 restraints weight = 14038.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.047942 restraints weight = 10760.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.048780 restraints weight = 8939.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.049398 restraints weight = 7807.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4300  Z= 0.146
  Angle     :  0.791  12.489   5935  Z= 0.397
  Chirality :  0.042   0.191    659
  Planarity :  0.003   0.028    686
  Dihedral  : 19.024  58.506    822
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 25.27 %
    Favored  : 72.34 %
  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: -0.25 (0.39), residues: 443
  helix:  0.70 (0.28), residues: 328
  sheet:  None (None), residues: 0
  loop : -2.67 (0.52), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 203 
 TYR   0.014   0.002   TYR D 219 
 PHE   0.027   0.001   PHE D 175 
 TRP   0.005   0.001   TRP D 198 
 HIS   0.005   0.001   HIS C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4300)
  covalent geometry    : angle       0.79068 ( 5935)
  hydrogen bonds       : bond        0.03931 (  259)
  hydrogen bonds       : angle       4.24931 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 GLU cc_start: 0.9629 (pp20) cc_final: 0.9374 (pp20)
REVERT: C   42 GLN cc_start: 0.9075 (pt0) cc_final: 0.8798 (pt0)
REVERT: C   43 MET cc_start: 0.9458 (mmm) cc_final: 0.9172 (mmm)
REVERT: C  126 GLN cc_start: 0.9414 (tt0) cc_final: 0.8733 (tp40)
REVERT: C  130 PHE cc_start: 0.9470 (m-10) cc_final: 0.8905 (m-80)
REVERT: C  138 TYR cc_start: 0.8893 (t80) cc_final: 0.8451 (t80)
REVERT: C  149 ASP cc_start: 0.9589 (m-30) cc_final: 0.9319 (p0)
REVERT: C  181 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8773 (mt-10)
REVERT: D  110 MET cc_start: 0.7804 (tpt) cc_final: 0.7417 (tpt)
REVERT: D  147 GLN cc_start: 0.8940 (mp10) cc_final: 0.8544 (mp10)
REVERT: D  199 LEU cc_start: 0.9537 (tp) cc_final: 0.9309 (pp)
  outliers start: 9
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0611
  time to fit residues: 6.3166
Evaluate side-chains
  79 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  142 HIS
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  117 HIS
Chi-restraints excluded: chain D residue  170 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 117 HIS
** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.064425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.044444 restraints weight = 20520.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.045953 restraints weight = 13944.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.047042 restraints weight = 10782.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.047834 restraints weight = 8983.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.048313 restraints weight = 7872.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   4300  Z= 0.171
  Angle     :  0.852  11.940   5935  Z= 0.426
  Chirality :  0.044   0.265    659
  Planarity :  0.004   0.029    686
  Dihedral  : 19.055  59.239    822
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 25.27 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.39), residues: 443
  helix:  0.55 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.53 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.012   0.002   TYR D 219 
 PHE   0.017   0.001   PHE D 175 
 TRP   0.003   0.001   TRP C 198 
 HIS   0.005   0.001   HIS C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 4300)
  covalent geometry    : angle       0.85220 ( 5935)
  hydrogen bonds       : bond        0.04283 (  259)
  hydrogen bonds       : angle       4.49084 (  747)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.9605 (tmm) cc_final: 0.9227 (ppp)
REVERT: C   37 GLU cc_start: 0.9639 (pp20) cc_final: 0.9393 (pp20)
REVERT: C   42 GLN cc_start: 0.9097 (pt0) cc_final: 0.8856 (pt0)
REVERT: C   43 MET cc_start: 0.9470 (mmm) cc_final: 0.9175 (mmm)
REVERT: C  126 GLN cc_start: 0.9429 (tt0) cc_final: 0.8790 (tp-100)
REVERT: C  130 PHE cc_start: 0.9509 (m-10) cc_final: 0.9039 (m-80)
REVERT: C  149 ASP cc_start: 0.9576 (m-30) cc_final: 0.9307 (p0)
REVERT: C  181 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8815 (mt-10)
REVERT: D   35 MET cc_start: 0.9552 (ppp) cc_final: 0.9309 (ppp)
REVERT: D  110 MET cc_start: 0.7819 (tpt) cc_final: 0.7410 (tpt)
REVERT: D  147 GLN cc_start: 0.8961 (mp10) cc_final: 0.8564 (mp10)
REVERT: D  199 LEU cc_start: 0.9531 (tp) cc_final: 0.9305 (pp)
  outliers start: 10
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0631
  time to fit residues: 6.2042
Evaluate side-chains
  78 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  142 HIS
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  242 GLN
Chi-restraints excluded: chain D residue   76 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.064295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.044674 restraints weight = 20591.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.046156 restraints weight = 14066.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.047230 restraints weight = 10885.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.048001 restraints weight = 9084.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.048563 restraints weight = 7969.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.150   4300  Z= 0.242
  Angle     :  1.288  59.172   5935  Z= 0.725
  Chirality :  0.045   0.273    659
  Planarity :  0.004   0.032    686
  Dihedral  : 19.062  59.243    822
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 25.80 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.23 %
  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: -0.43 (0.39), residues: 443
  helix:  0.52 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.53 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  94 
 TYR   0.012   0.002   TYR D 219 
 PHE   0.015   0.001   PHE D 175 
 TRP   0.002   0.001   TRP C 198 
 HIS   0.005   0.001   HIS C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 4300)
  covalent geometry    : angle       1.28837 ( 5935)
  hydrogen bonds       : bond        0.04334 (  259)
  hydrogen bonds       : angle       4.52075 (  747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 949.39 seconds
wall clock time: 16 minutes 57.75 seconds (1017.75 seconds total)