Starting phenix.real_space_refine
on Wed Sep 17 06:12:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yo1_39433/09_2025/8yo1_39433.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yo1_39433/09_2025/8yo1_39433.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yo1_39433/09_2025/8yo1_39433.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yo1_39433/09_2025/8yo1_39433.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yo1_39433/09_2025/8yo1_39433.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yo1_39433/09_2025/8yo1_39433.cif"
  }
  resolution = 3.55
  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=   0.051
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    3744      2.51       5
     N    1048      2.21       5
     O    1134      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5969
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2953
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 13, 'TRANS': 359}
    Chain: "D"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2953
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 13, 'TRANS': 359}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.77, per 1000 atoms: 0.30
  Number of scatterers: 5969
  At special positions: 0
  Unit cell: (64.48, 86.32, 94.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       6     15.00
     Mg      1     11.99
     O    1134      8.00
     N    1048      7.00
     C    3744      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: 0.53
  Conformation dependent library (CDL) restraints added in 399.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      39.4% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'C' and resid 10 through 18
    Processing helix  chain 'C' and resid 18 through 24
      removed outlier: 4.082A  pdb=" N   TYR C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 66
      removed outlier: 3.551A  pdb=" N   VAL C  49 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR C  66 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 114
    Processing helix  chain 'C' and resid 136 through 143
      removed outlier: 3.641A  pdb=" N   ASN C 141 " --> pdb=" O   SER C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 216
      removed outlier: 3.663A  pdb=" N   LEU C 202 " --> pdb=" O   SER C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 240
      removed outlier: 3.759A  pdb=" N   TYR C 239 " --> pdb=" O   TYR C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 300
      removed outlier: 3.604A  pdb=" N   ASP C 290 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      Proline residue:  C 293  - end of helix
    Processing helix  chain 'C' and resid 304 through 310
      removed outlier: 3.503A  pdb=" N   VAL C 308 " --> pdb=" O   THR C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 345
    Processing helix  chain 'C' and resid 348 through 359
      removed outlier: 3.597A  pdb=" N   ILE C 352 " --> pdb=" O   ASP C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 373
      removed outlier: 3.811A  pdb=" N   LEU C 363 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET C 364 " --> pdb=" O   GLU C 360 " (cutoff:3.500A)
      Proline residue:  C 365  - end of helix
    Processing helix  chain 'D' and resid 10 through 18
    Processing helix  chain 'D' and resid 19 through 22
    Processing helix  chain 'D' and resid 45 through 66
      removed outlier: 3.637A  pdb=" N   VAL D  49 " --> pdb=" O   VAL D  45 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE D  55 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 114
      removed outlier: 3.785A  pdb=" N   ILE D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 143
    Processing helix  chain 'D' and resid 198 through 216
      removed outlier: 3.501A  pdb=" N   LEU D 202 " --> pdb=" O   SER D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 240
      removed outlier: 3.794A  pdb=" N   TYR D 239 " --> pdb=" O   TYR D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 300
      removed outlier: 3.724A  pdb=" N   ASP D 290 " --> pdb=" O   ASP D 286 " (cutoff:3.500A)
      Proline residue:  D 293  - end of helix
    Processing helix  chain 'D' and resid 304 through 310
    Processing helix  chain 'D' and resid 337 through 345
    Processing helix  chain 'D' and resid 348 through 358
      removed outlier: 3.804A  pdb=" N   ILE D 352 " --> pdb=" O   ASP D 348 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 362 through 373
      removed outlier: 3.824A  pdb=" N   ILE D 366 " --> pdb=" O   ILE D 362 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 8
    Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 31
    Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 35
    Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 175
      removed outlier: 5.219A  pdb=" N   ASN C 156 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   MET C 146 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98
      removed outlier: 3.851A  pdb=" N   VAL C  97 " --> pdb=" O   ILE C 105 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA7, first strand: chain 'C' and resid 244 through 247
      removed outlier: 7.106A  pdb=" N   ARG C 263 " --> pdb=" O   ILE C 314 " (cutoff:3.500A)
      removed outlier: 8.624A  pdb=" N   MET C 316 " --> pdb=" O   ARG C 263 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LEU C 265 " --> pdb=" O   MET C 316 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   VAL C 318 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   TYR C 267 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 35
    Processing sheet with id=AA9, first strand: chain 'D' and resid 168 through 175
      removed outlier: 5.734A  pdb=" N   ASN D 156 " --> pdb=" O   ASP D 153 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP D 153 " --> pdb=" O   ASN D 156 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET D 146 " --> pdb=" O   ILE D 186 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 97 through 98
    Processing sheet with id=AB2, first strand: chain 'D' and resid 244 through 247
      removed outlier: 7.245A  pdb=" N   ARG D 263 " --> pdb=" O   ILE D 314 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   MET D 316 " --> pdb=" O   ARG D 263 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU D 265 " --> pdb=" O   MET D 316 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   VAL D 318 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   TYR D 267 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1015
        1.31 -     1.44: 1513
        1.44 -     1.56: 3475
        1.56 -     1.69: 7
        1.69 -     1.81: 66
  Bond restraints: 6076
  Sorted by residual:
  bond pdb=" N   ASN C 141 "
       pdb=" CA  ASN C 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.381  0.077 1.16e-02 7.43e+03 4.45e+01
  bond pdb=" CA  ASN C 141 "
       pdb=" C   ASN C 141 "
    ideal  model  delta    sigma   weight residual
    1.524  1.450  0.074 1.28e-02 6.10e+03 3.36e+01
  bond pdb=" O3A ANP D 701 "
       pdb=" PB  ANP D 701 "
    ideal  model  delta    sigma   weight residual
    1.700  1.586  0.114 2.00e-02 2.50e+03 3.27e+01
  bond pdb=" O3A ANP C 701 "
       pdb=" PB  ANP C 701 "
    ideal  model  delta    sigma   weight residual
    1.700  1.611  0.089 2.00e-02 2.50e+03 1.97e+01
  bond pdb=" CA  SER C 138 "
       pdb=" C   SER C 138 "
    ideal  model  delta    sigma   weight residual
    1.524  1.462  0.062 1.44e-02 4.82e+03 1.83e+01
  ... (remaining 6071 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.50: 8118
        3.50 -     7.00: 69
        7.00 -    10.49: 11
       10.49 -    13.99: 1
       13.99 -    17.49: 1
  Bond angle restraints: 8200
  Sorted by residual:
  angle pdb=" N   SER C 137 "
        pdb=" CA  SER C 137 "
        pdb=" C   SER C 137 "
      ideal   model   delta    sigma   weight residual
     111.07   97.72   13.35 1.07e+00 8.73e-01 1.56e+02
  angle pdb=" N   GLY C 136 "
        pdb=" CA  GLY C 136 "
        pdb=" C   GLY C 136 "
      ideal   model   delta    sigma   weight residual
     113.18  130.67  -17.49 2.37e+00 1.78e-01 5.45e+01
  angle pdb=" N   LEU C 139 "
        pdb=" CA  LEU C 139 "
        pdb=" C   LEU C 139 "
      ideal   model   delta    sigma   weight residual
     111.28  118.77   -7.49 1.09e+00 8.42e-01 4.73e+01
  angle pdb=" N   ASN C 141 "
        pdb=" CA  ASN C 141 "
        pdb=" C   ASN C 141 "
      ideal   model   delta    sigma   weight residual
     111.02  103.35    7.67 1.22e+00 6.72e-01 3.95e+01
  angle pdb=" N   VAL D 128 "
        pdb=" CA  VAL D 128 "
        pdb=" C   VAL D 128 "
      ideal   model   delta    sigma   weight residual
     112.17  106.49    5.68 9.50e-01 1.11e+00 3.58e+01
  ... (remaining 8195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.82: 3542
       29.82 -    59.64: 167
       59.64 -    89.45: 13
       89.45 -   119.27: 1
      119.27 -   149.09: 1
  Dihedral angle restraints: 3724
    sinusoidal: 1590
      harmonic: 2134
  Sorted by residual:
  dihedral pdb=" O1B ANP C 701 "
           pdb=" N3B ANP C 701 "
           pdb=" PB  ANP C 701 "
           pdb=" PG  ANP C 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15 -175.76 -149.09     1      3.00e+01 1.11e-03 1.98e+01
  dihedral pdb=" C   ASN C 141 "
           pdb=" N   ASN C 141 "
           pdb=" CA  ASN C 141 "
           pdb=" CB  ASN C 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.18   -9.42     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" O1A ANP C 701 "
           pdb=" O3A ANP C 701 "
           pdb=" PA  ANP C 701 "
           pdb=" PB  ANP C 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  178.40  -95.29     1      3.00e+01 1.11e-03 1.16e+01
  ... (remaining 3721 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 739
       0.060 -    0.121: 144
       0.121 -    0.181: 18
       0.181 -    0.241: 4
       0.241 -    0.302: 1
  Chirality restraints: 906
  Sorted by residual:
  chirality pdb=" CA  LEU C 139 "
            pdb=" N   LEU C 139 "
            pdb=" C   LEU C 139 "
            pdb=" CB  LEU C 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  SER C 137 "
            pdb=" N   SER C 137 "
            pdb=" C   SER C 137 "
            pdb=" CB  SER C 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  VAL C 135 "
            pdb=" N   VAL C 135 "
            pdb=" C   VAL C 135 "
            pdb=" CB  VAL C 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 903 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 136 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   GLY C 136 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   GLY C 136 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER C 137 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 134 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.07e+00
        pdb=" C   GLY C 134 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLY C 134 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL C 135 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 105 "   -0.036 5.00e-02 4.00e+02   5.42e-02 4.70e+00
        pdb=" N   PRO D 106 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D 106 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 106 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 136
        2.67 -     3.23: 5828
        3.23 -     3.79: 9495
        3.79 -     4.34: 12765
        4.34 -     4.90: 21016
  Nonbonded interactions: 49240
  Sorted by model distance:
  nonbonded pdb=" O   THR D 140 "
            pdb=" OG  SER D 144 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   VAL C 109 "
            pdb=" OG1 THR C 113 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OH  TYR C  22 "
            pdb=" OH  TYR D  22 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   TRP D 112 "
            pdb=" ND2 ASN D 141 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" ND2 ASN D  28 "
            pdb=" O   GLU D 193 "
     model   vdw
     2.221 3.120
  ... (remaining 49235 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 1 through 701)
  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:             0.540
  Set stop_for_unknowns flag:              0.010
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.640
  Find NCS groups from input model:        0.060
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
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      :  0.006   0.114   6076  Z= 0.318
  Angle     :  0.807  17.490   8200  Z= 0.432
  Chirality :  0.050   0.302    906
  Planarity :  0.005   0.054   1056
  Dihedral  : 16.112 149.087   2348
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 20.49 %
    Favored  : 79.05 %
  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 aren not related in a simple way.
  whole: -0.33 (0.31), residues: 742
  helix:  0.92 (0.32), residues: 254
  sheet:  0.16 (0.43), residues: 130
  loop : -1.21 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 182 
 TYR   0.004   0.001   TYR D  44 
 PHE   0.026   0.001   PHE D 221 
 TRP   0.012   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 6076)
  covalent geometry    : angle       0.80672 ( 8200)
  hydrogen bonds       : bond        0.12675 (  280)
  hydrogen bonds       : angle       6.15580 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.231 
Fit side-chains
REVERT: C  142 ILE cc_start: 0.4883 (OUTLIER) cc_final: 0.4446 (tt)
REVERT: C  310 GLU cc_start: 0.5848 (pt0) cc_final: 0.5362 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 100
  average time/residue: 0.0895
  time to fit residues: 11.8451
Evaluate side-chains
  96 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain D residue  156 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
D  75 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.237738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.199527 restraints weight = 5575.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.201007 restraints weight = 4554.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.204600 restraints weight = 3582.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.205986 restraints weight = 2612.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.206394 restraints weight = 2406.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.0850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6076  Z= 0.139
  Angle     :  0.545   6.865   8200  Z= 0.286
  Chirality :  0.047   0.181    906
  Planarity :  0.005   0.058   1056
  Dihedral  :  9.703 107.551    866
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.50 %
    Favored  : 79.05 %
  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 aren not related in a simple way.
  whole: -0.29 (0.31), residues: 742
  helix:  0.74 (0.31), residues: 258
  sheet:  0.30 (0.44), residues: 124
  loop : -1.04 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 127 
 TYR   0.008   0.002   TYR D 239 
 PHE   0.022   0.002   PHE D 221 
 TRP   0.007   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6076)
  covalent geometry    : angle       0.54500 ( 8200)
  hydrogen bonds       : bond        0.03547 (  280)
  hydrogen bonds       : angle       5.15095 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.243 
Fit side-chains
REVERT: C  182 ARG cc_start: 0.6909 (mmt180) cc_final: 0.6419 (mtp85)
REVERT: C  237 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.6917 (mtm110)
REVERT: D    1 MET cc_start: 0.7029 (tpp) cc_final: 0.6651 (tpt)
REVERT: D   34 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4557 (m-10)
REVERT: D  324 MET cc_start: 0.5977 (ptt) cc_final: 0.5735 (ptt)
  outliers start: 16
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0988
  time to fit residues: 13.6807
Evaluate side-chains
  100 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.221172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.184902 restraints weight = 5703.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.187810 restraints weight = 5015.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.189068 restraints weight = 4212.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.190524 restraints weight = 3292.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.190879 restraints weight = 2840.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.083   6076  Z= 0.375
  Angle     :  0.810   7.790   8200  Z= 0.424
  Chirality :  0.058   0.271    906
  Planarity :  0.006   0.065   1056
  Dihedral  :  9.459  84.123    860
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 20.18 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.30), residues: 742
  helix: -0.19 (0.32), residues: 246
  sheet: -0.44 (0.43), residues: 120
  loop : -1.33 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 208 
 TYR   0.019   0.003   TYR D 267 
 PHE   0.033   0.003   PHE C 147 
 TRP   0.013   0.003   TRP C  39 
 HIS   0.007   0.002   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00881 ( 6076)
  covalent geometry    : angle       0.81008 ( 8200)
  hydrogen bonds       : bond        0.04859 (  280)
  hydrogen bonds       : angle       5.85795 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7065 (mmm) cc_final: 0.6363 (ttt)
REVERT: C   92 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.5952 (mm)
REVERT: C  182 ARG cc_start: 0.6997 (mmt180) cc_final: 0.6773 (tpt90)
REVERT: C  237 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7239 (mtm110)
REVERT: C  311 CYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5868 (t)
REVERT: C  323 ASN cc_start: 0.7669 (m-40) cc_final: 0.7435 (m-40)
REVERT: C  356 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7300 (tt)
REVERT: D    1 MET cc_start: 0.7019 (tpp) cc_final: 0.6164 (ttt)
REVERT: D   34 PHE cc_start: 0.5626 (OUTLIER) cc_final: 0.4213 (m-10)
REVERT: D  104 GLU cc_start: 0.5892 (mm-30) cc_final: 0.5458 (mm-30)
  outliers start: 28
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0838
  time to fit residues: 13.7684
Evaluate side-chains
  113 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  287 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.232331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.196315 restraints weight = 5593.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.199107 restraints weight = 4272.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.201694 restraints weight = 3204.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.202504 restraints weight = 2522.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.202920 restraints weight = 2394.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6076  Z= 0.136
  Angle     :  0.555   7.434   8200  Z= 0.294
  Chirality :  0.048   0.172    906
  Planarity :  0.005   0.059   1056
  Dihedral  :  8.304  87.458    860
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.63 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.30), residues: 742
  helix:  0.36 (0.32), residues: 248
  sheet:  0.00 (0.44), residues: 118
  loop : -1.05 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  65 
 TYR   0.007   0.001   TYR C  22 
 PHE   0.019   0.001   PHE D 221 
 TRP   0.009   0.001   TRP C  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6076)
  covalent geometry    : angle       0.55490 ( 8200)
  hydrogen bonds       : bond        0.03521 (  280)
  hydrogen bonds       : angle       5.16830 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.236 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7001 (mmm) cc_final: 0.6377 (ttt)
REVERT: C   92 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5915 (mm)
REVERT: C  182 ARG cc_start: 0.6898 (mmt180) cc_final: 0.6624 (tpt90)
REVERT: C  237 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7127 (mtm110)
REVERT: C  311 CYS cc_start: 0.6314 (OUTLIER) cc_final: 0.6044 (t)
REVERT: C  323 ASN cc_start: 0.7376 (m-40) cc_final: 0.7102 (m-40)
REVERT: D    1 MET cc_start: 0.6829 (tpp) cc_final: 0.6050 (ttt)
REVERT: D   34 PHE cc_start: 0.5379 (OUTLIER) cc_final: 0.4429 (m-10)
REVERT: D  104 GLU cc_start: 0.5752 (mm-30) cc_final: 0.5470 (mm-30)
REVERT: D  321 MET cc_start: 0.7409 (tpt) cc_final: 0.6687 (ttm)
  outliers start: 19
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0892
  time to fit residues: 13.5530
Evaluate side-chains
  112 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  132 MET
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0370
   chunk 20 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
D  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.231068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.194862 restraints weight = 5665.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.198158 restraints weight = 4409.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.200172 restraints weight = 3236.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.200728 restraints weight = 2589.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.204678 restraints weight = 2466.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6076  Z= 0.152
  Angle     :  0.554   7.575   8200  Z= 0.292
  Chirality :  0.048   0.174    906
  Planarity :  0.005   0.057   1056
  Dihedral  :  8.104  88.915    860
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.10 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.30), residues: 742
  helix:  0.46 (0.32), residues: 248
  sheet:  0.01 (0.44), residues: 128
  loop : -1.00 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 127 
 TYR   0.007   0.001   TYR D 267 
 PHE   0.017   0.002   PHE D 221 
 TRP   0.008   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6076)
  covalent geometry    : angle       0.55430 ( 8200)
  hydrogen bonds       : bond        0.03452 (  280)
  hydrogen bonds       : angle       5.13800 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.233 
Fit side-chains
REVERT: C    1 MET cc_start: 0.6966 (mmm) cc_final: 0.6345 (ttt)
REVERT: C   92 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.5936 (mm)
REVERT: C  182 ARG cc_start: 0.6936 (mmt180) cc_final: 0.6571 (tpt90)
REVERT: C  237 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7063 (mtm110)
REVERT: C  311 CYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5968 (t)
REVERT: D    1 MET cc_start: 0.6844 (tpp) cc_final: 0.6109 (ttt)
REVERT: D   34 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4530 (m-10)
REVERT: D  321 MET cc_start: 0.7374 (tpt) cc_final: 0.6607 (ttm)
REVERT: D  358 ASN cc_start: 0.7226 (m-40) cc_final: 0.7001 (m-40)
  outliers start: 28
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0852
  time to fit residues: 13.5435
Evaluate side-chains
  118 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  132 MET
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0170
   chunk 40 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0770
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.235383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.198705 restraints weight = 5539.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.202702 restraints weight = 4683.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.205197 restraints weight = 3223.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.205681 restraints weight = 2457.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.208383 restraints weight = 2363.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6539
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6076  Z= 0.119
  Angle     :  0.548  10.140   8200  Z= 0.286
  Chirality :  0.048   0.334    906
  Planarity :  0.004   0.057   1056
  Dihedral  :  7.757  89.959    860
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.56 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.30), residues: 742
  helix:  0.70 (0.32), residues: 248
  sheet:  0.23 (0.44), residues: 128
  loop : -0.95 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  65 
 TYR   0.005   0.001   TYR C  22 
 PHE   0.021   0.001   PHE C 232 
 TRP   0.009   0.001   TRP D  39 
 HIS   0.005   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6076)
  covalent geometry    : angle       0.54827 ( 8200)
  hydrogen bonds       : bond        0.03189 (  280)
  hydrogen bonds       : angle       4.95009 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.213 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7014 (mmm) cc_final: 0.6431 (ttt)
REVERT: C   92 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.5887 (mm)
REVERT: C  182 ARG cc_start: 0.6932 (mmt180) cc_final: 0.6595 (tpt90)
REVERT: C  237 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7026 (mtm110)
REVERT: C  311 CYS cc_start: 0.6282 (t) cc_final: 0.5996 (t)
REVERT: D    1 MET cc_start: 0.6956 (tpp) cc_final: 0.6194 (ttt)
REVERT: D   34 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.4593 (m-10)
REVERT: D  321 MET cc_start: 0.7442 (tpt) cc_final: 0.6670 (ttm)
REVERT: D  344 HIS cc_start: 0.7141 (t-90) cc_final: 0.6388 (t-170)
REVERT: D  358 ASN cc_start: 0.7258 (m-40) cc_final: 0.7008 (m-40)
  outliers start: 24
  outliers final: 13
  residues processed: 120
  average time/residue: 0.0810
  time to fit residues: 13.0194
Evaluate side-chains
  111 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  146 MET
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 72 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.234801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.198432 restraints weight = 5556.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.202557 restraints weight = 4564.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.204915 restraints weight = 3138.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.207287 restraints weight = 2415.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.207698 restraints weight = 2179.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6076  Z= 0.124
  Angle     :  0.566  17.090   8200  Z= 0.288
  Chirality :  0.047   0.142    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.662  89.875    860
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 22.02 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.31), residues: 742
  helix:  0.87 (0.32), residues: 256
  sheet:  0.38 (0.45), residues: 128
  loop : -0.98 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 127 
 TYR   0.004   0.001   TYR D 267 
 PHE   0.018   0.002   PHE D 221 
 TRP   0.009   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6076)
  covalent geometry    : angle       0.56617 ( 8200)
  hydrogen bonds       : bond        0.03224 (  280)
  hydrogen bonds       : angle       4.91908 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.236 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7051 (mmm) cc_final: 0.6446 (ttt)
REVERT: C  182 ARG cc_start: 0.6960 (mmt180) cc_final: 0.6577 (tpt90)
REVERT: C  311 CYS cc_start: 0.6323 (OUTLIER) cc_final: 0.6020 (t)
REVERT: D   34 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.4645 (m-10)
REVERT: D  358 ASN cc_start: 0.7247 (m-40) cc_final: 0.6981 (m-40)
  outliers start: 22
  outliers final: 13
  residues processed: 113
  average time/residue: 0.0821
  time to fit residues: 12.3346
Evaluate side-chains
  110 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    0.0570
   chunk 39 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0870
   chunk 20 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
C 269 ASN
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.238177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.201627 restraints weight = 5523.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.206059 restraints weight = 4564.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.208722 restraints weight = 3091.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.211561 restraints weight = 2343.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.211938 restraints weight = 2114.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6076  Z= 0.112
  Angle     :  0.559  17.721   8200  Z= 0.283
  Chirality :  0.046   0.141    906
  Planarity :  0.004   0.058   1056
  Dihedral  :  7.471  88.659    860
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.70 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.31), residues: 742
  helix:  1.07 (0.32), residues: 256
  sheet:  0.53 (0.45), residues: 128
  loop : -0.98 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 127 
 TYR   0.006   0.001   TYR C  22 
 PHE   0.016   0.001   PHE C 143 
 TRP   0.007   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6076)
  covalent geometry    : angle       0.55911 ( 8200)
  hydrogen bonds       : bond        0.03042 (  280)
  hydrogen bonds       : angle       4.81243 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.167 
Fit side-chains
REVERT: C    1 MET cc_start: 0.6971 (mmm) cc_final: 0.6433 (ttt)
REVERT: C  182 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6443 (mtp85)
REVERT: C  311 CYS cc_start: 0.6302 (OUTLIER) cc_final: 0.6011 (t)
REVERT: D   34 PHE cc_start: 0.5327 (OUTLIER) cc_final: 0.4619 (m-10)
REVERT: D  358 ASN cc_start: 0.7189 (m-40) cc_final: 0.6898 (m-40)
  outliers start: 17
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0848
  time to fit residues: 12.4825
Evaluate side-chains
  108 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.236050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.199780 restraints weight = 5564.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.203924 restraints weight = 4501.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.206409 restraints weight = 3064.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.208954 restraints weight = 2395.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.209345 restraints weight = 2149.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6076  Z= 0.127
  Angle     :  0.560  17.109   8200  Z= 0.286
  Chirality :  0.047   0.143    906
  Planarity :  0.004   0.058   1056
  Dihedral  :  7.495  86.753    860
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.39 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.31), residues: 742
  helix:  0.94 (0.31), residues: 258
  sheet:  0.56 (0.46), residues: 128
  loop : -1.01 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 127 
 TYR   0.012   0.001   TYR C 239 
 PHE   0.015   0.001   PHE D 221 
 TRP   0.006   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6076)
  covalent geometry    : angle       0.56021 ( 8200)
  hydrogen bonds       : bond        0.03086 (  280)
  hydrogen bonds       : angle       4.80809 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7041 (mmm) cc_final: 0.6490 (ttt)
REVERT: C   92 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5898 (mm)
REVERT: C  182 ARG cc_start: 0.6989 (mmt180) cc_final: 0.6595 (mtp85)
REVERT: C  311 CYS cc_start: 0.6363 (OUTLIER) cc_final: 0.6063 (t)
REVERT: D   34 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4614 (m-10)
REVERT: D  321 MET cc_start: 0.7444 (tpt) cc_final: 0.6371 (ttm)
  outliers start: 17
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0792
  time to fit residues: 11.7914
Evaluate side-chains
  109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0010
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 323 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.234644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.198004 restraints weight = 5589.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.202162 restraints weight = 4562.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.204657 restraints weight = 3100.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.207131 restraints weight = 2424.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.207644 restraints weight = 2164.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6076  Z= 0.142
  Angle     :  0.594  17.512   8200  Z= 0.303
  Chirality :  0.047   0.145    906
  Planarity :  0.004   0.058   1056
  Dihedral  :  7.526  84.372    860
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.70 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.31), residues: 742
  helix:  0.89 (0.31), residues: 258
  sheet:  0.57 (0.46), residues: 128
  loop : -1.02 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 127 
 TYR   0.022   0.001   TYR C 239 
 PHE   0.014   0.002   PHE C  36 
 TRP   0.005   0.001   TRP D  39 
 HIS   0.005   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6076)
  covalent geometry    : angle       0.59405 ( 8200)
  hydrogen bonds       : bond        0.03113 (  280)
  hydrogen bonds       : angle       4.81933 (  777)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.249 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7160 (mmm) cc_final: 0.6608 (ttt)
REVERT: C   92 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5804 (mm)
REVERT: C  182 ARG cc_start: 0.6997 (mmt180) cc_final: 0.6617 (mtp85)
REVERT: C  311 CYS cc_start: 0.6337 (OUTLIER) cc_final: 0.6021 (t)
REVERT: C  356 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7377 (tp)
REVERT: D   34 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.4643 (m-10)
REVERT: D  321 MET cc_start: 0.7477 (tpt) cc_final: 0.6598 (ttm)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0746
  time to fit residues: 10.8272
Evaluate side-chains
  110 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 264 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 = 0.4507 r_free = 0.4507 target = 0.231478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.195891 restraints weight = 5578.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.199102 restraints weight = 4281.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.201301 restraints weight = 3433.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.203391 restraints weight = 2546.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.203756 restraints weight = 2186.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6076  Z= 0.169
  Angle     :  0.607  17.246   8200  Z= 0.312
  Chirality :  0.049   0.151    906
  Planarity :  0.005   0.057   1056
  Dihedral  :  7.817  84.364    860
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.85 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.31), residues: 742
  helix:  0.78 (0.32), residues: 256
  sheet:  0.47 (0.46), residues: 128
  loop : -1.05 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 127 
 TYR   0.022   0.002   TYR C 239 
 PHE   0.015   0.002   PHE D 147 
 TRP   0.005   0.001   TRP C  39 
 HIS   0.005   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6076)
  covalent geometry    : angle       0.60700 ( 8200)
  hydrogen bonds       : bond        0.03305 (  280)
  hydrogen bonds       : angle       4.92742 (  777)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1067.12 seconds
wall clock time: 19 minutes 17.15 seconds (1157.15 seconds total)