Starting phenix.real_space_refine
on Sat May 10 06:15:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exr_28660/05_2025/8exr_28660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exr_28660/05_2025/8exr_28660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exr_28660/05_2025/8exr_28660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exr_28660/05_2025/8exr_28660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exr_28660/05_2025/8exr_28660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exr_28660/05_2025/8exr_28660.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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
     Zn      2      6.06       5
     P       5      5.49       5
     S      20      5.16       5
     C    3438      2.51       5
     N     802      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5111
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2496
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 6, 'TRANS': 288}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 2051
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 6, 'TRANS': 234}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 445
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.38, per 1000 atoms: 0.66
  Number of scatterers: 5111
  At special positions: 0
  Unit cell: (72.38, 85.47, 93.94, 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)
     Zn      2     29.99
     S      20     16.00
     P       5     15.00
     O     844      8.00
     N     802      7.00
     C    3438      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: 1.28
  Conformation dependent library (CDL) restraints added in 499.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "


  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      70.7% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 3.858A  pdb=" N   TYR B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 48
      removed outlier: 4.065A  pdb=" N   LEU B  43 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 100 through 133
      removed outlier: 4.624A  pdb=" N   VAL B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 194 through 208
      removed outlier: 4.327A  pdb=" N   LEU B 200 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ASN B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.197A  pdb=" N   ILE B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 251
      removed outlier: 3.501A  pdb=" N   ILE B 232 " --> pdb=" O   PRO B 228 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ILE B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   HIS B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 271
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 329
      removed outlier: 3.534A  pdb=" N   PHE B 328 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 336
    Processing helix  chain 'A' and resid 2 through 31
      removed outlier: 3.529A  pdb=" N   ILE A  15 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 47
      removed outlier: 4.125A  pdb=" N   LEU A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.566A  pdb=" N   VAL A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 194 through 208
      removed outlier: 3.814A  pdb=" N   ASN A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 227 through 251
      removed outlier: 3.857A  pdb=" N   HIS A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LYS A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG A 235 " --> pdb=" O   HIS A 231 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 253
      No H-bonds generated for 'chain 'A' and resid 252 through 253'
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 257 through 271
      removed outlier: 3.752A  pdb=" N   VAL A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 299
      removed outlier: 3.734A  pdb=" N   LYS C 299 " --> pdb=" O   LEU C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 329
      removed outlier: 4.354A  pdb=" N   LEU C 311 " --> pdb=" O   SER C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 336
      removed outlier: 4.040A  pdb=" N   THR C 335 " --> pdb=" O   GLN C 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 164
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.685A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)

    299 hydrogen bonds defined for protein.
    870 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: 1.36

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.18 -     1.33: 1301
        1.33 -     1.47: 1570
        1.47 -     1.61: 2315
        1.61 -     1.75: 3
        1.75 -     1.89: 34
  Bond restraints: 5223
  Sorted by residual:
  bond pdb=" CB  HIS B 213 "
       pdb=" CG  HIS B 213 "
    ideal  model  delta    sigma   weight residual
    1.497  1.371  0.126 1.40e-02 5.10e+03 8.05e+01
  bond pdb=" CB  HIS B 153 "
       pdb=" CG  HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.372  0.125 1.40e-02 5.10e+03 7.94e+01
  bond pdb=" CB  PHE A 173 "
       pdb=" CG  PHE A 173 "
    ideal  model  delta    sigma   weight residual
    1.502  1.321  0.181 2.30e-02 1.89e+03 6.18e+01
  bond pdb=" NE1 TRP B  39 "
       pdb=" CE2 TRP B  39 "
    ideal  model  delta    sigma   weight residual
    1.370  1.285  0.085 1.10e-02 8.26e+03 6.00e+01
  bond pdb=" CB  HIS A 205 "
       pdb=" CG  HIS A 205 "
    ideal  model  delta    sigma   weight residual
    1.497  1.389  0.108 1.40e-02 5.10e+03 5.93e+01
  ... (remaining 5218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 6387
        3.28 -     6.57: 574
        6.57 -     9.85: 51
        9.85 -    13.13: 6
       13.13 -    16.42: 3
  Bond angle restraints: 7021
  Sorted by residual:
  angle pdb=" N   VAL A 160 "
        pdb=" CA  VAL A 160 "
        pdb=" C   VAL A 160 "
      ideal   model   delta    sigma   weight residual
     108.46  122.06  -13.60 1.49e+00 4.50e-01 8.33e+01
  angle pdb=" N   ARG A 194 "
        pdb=" CA  ARG A 194 "
        pdb=" C   ARG A 194 "
      ideal   model   delta    sigma   weight residual
     114.04  102.97   11.07 1.24e+00 6.50e-01 7.97e+01
  angle pdb=" N   VAL B 160 "
        pdb=" CA  VAL B 160 "
        pdb=" C   VAL B 160 "
      ideal   model   delta    sigma   weight residual
     108.46  121.66  -13.20 1.49e+00 4.50e-01 7.84e+01
  angle pdb=" CA  PHE B  30 "
        pdb=" CB  PHE B  30 "
        pdb=" CG  PHE B  30 "
      ideal   model   delta    sigma   weight residual
     113.80  105.18    8.62 1.00e+00 1.00e+00 7.44e+01
  angle pdb=" N   TRP B 174 "
        pdb=" CA  TRP B 174 "
        pdb=" C   TRP B 174 "
      ideal   model   delta    sigma   weight residual
     110.56  126.98  -16.42 1.94e+00 2.66e-01 7.16e+01
  ... (remaining 7016 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.09: 2907
       14.09 -    28.17: 148
       28.17 -    42.25: 49
       42.25 -    56.34: 30
       56.34 -    70.42: 11
  Dihedral angle restraints: 3145
    sinusoidal: 1362
      harmonic: 1783
  Sorted by residual:
  dihedral pdb=" C   PHE B 258 "
           pdb=" N   PHE B 258 "
           pdb=" CA  PHE B 258 "
           pdb=" CB  PHE B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.82   -7.78     0      2.50e+00 1.60e-01 9.68e+00
  dihedral pdb=" N   TYR B 155 "
           pdb=" C   TYR B 155 "
           pdb=" CA  TYR B 155 "
           pdb=" CB  TYR B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.57   -7.77     0      2.50e+00 1.60e-01 9.66e+00
  dihedral pdb=" CG  ARG A 235 "
           pdb=" CD  ARG A 235 "
           pdb=" NE  ARG A 235 "
           pdb=" CZ  ARG A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  143.09   36.91     2      1.50e+01 4.44e-03 7.69e+00
  ... (remaining 3142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 564
       0.117 -    0.234: 200
       0.234 -    0.351: 31
       0.351 -    0.468: 4
       0.468 -    0.584: 1
  Chirality restraints: 800
  Sorted by residual:
  chirality pdb=" C5  P6L A 702 "
            pdb=" C6  P6L A 702 "
            pdb=" C7  P6L A 702 "
            pdb=" O4  P6L A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.73   -0.58 2.00e-01 2.50e+01 8.54e+00
  chirality pdb=" CA  TRP B 174 "
            pdb=" N   TRP B 174 "
            pdb=" C   TRP B 174 "
            pdb=" CB  TRP B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CA  TYR B 155 "
            pdb=" N   TYR B 155 "
            pdb=" C   TYR B 155 "
            pdb=" CB  TYR B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 797 not shown)

  Planarity restraints: 823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 P6L B 702 "    0.079 2.00e-02 2.50e+03   1.61e-01 2.59e+02
        pdb=" C22 P6L B 702 "   -0.213 2.00e-02 2.50e+03
        pdb=" C23 P6L B 702 "    0.213 2.00e-02 2.50e+03
        pdb=" C24 P6L B 702 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 P6L A 702 "    0.077 2.00e-02 2.50e+03   1.53e-01 2.35e+02
        pdb=" C22 P6L A 702 "   -0.203 2.00e-02 2.50e+03
        pdb=" C23 P6L A 702 "    0.203 2.00e-02 2.50e+03
        pdb=" C24 P6L A 702 "   -0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C32 P6L A 702 "   -0.074 2.00e-02 2.50e+03   1.48e-01 2.18e+02
        pdb=" C33 P6L A 702 "    0.195 2.00e-02 2.50e+03
        pdb=" C34 P6L A 702 "   -0.195 2.00e-02 2.50e+03
        pdb=" C35 P6L A 702 "    0.074 2.00e-02 2.50e+03
  ... (remaining 820 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 76
        2.59 -     3.17: 5122
        3.17 -     3.75: 7615
        3.75 -     4.32: 10357
        4.32 -     4.90: 15033
  Nonbonded interactions: 38203
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.016 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.017 2.230
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.038 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.050 2.230
  nonbonded pdb=" O   GLY B 286 "
            pdb=" CG  LYS B 287 "
     model   vdw
     2.142 3.440
  ... (remaining 38198 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.660
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
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      :  0.026   0.181   5227  Z= 1.487
  Angle     :  1.944  16.416   7021  Z= 1.328
  Chirality :  0.115   0.584    800
  Planarity :  0.013   0.161    823
  Dihedral  : 12.156  70.423   1981
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.76 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.32), residues: 580
  helix: -0.13 (0.24), residues: 383
  sheet: -0.25 (0.87), residues: 26
  loop : -0.87 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.009   TRP B  99 
 HIS   0.012   0.003   HIS A 153 
 PHE   0.033   0.006   PHE B 284 
 TYR   0.099   0.012   TYR A 203 
 ARG   0.006   0.001   ARG A  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25172 (  299)
  hydrogen bonds       : angle       8.15000 (  870)
  metal coordination   : bond        0.05433 (    4)
  covalent geometry    : bond        0.02593 ( 5223)
  covalent geometry    : angle       1.94400 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 LEU cc_start: 0.8542 (mt) cc_final: 0.7864 (tt)
REVERT: B  136 LEU cc_start: 0.6840 (tp) cc_final: 0.6454 (tp)
REVERT: B  255 LYS cc_start: 0.8736 (mttt) cc_final: 0.8205 (mmtm)
REVERT: A  141 ASN cc_start: 0.7362 (m-40) cc_final: 0.6924 (p0)
REVERT: A  187 PHE cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80)
REVERT: A  219 ILE cc_start: 0.8605 (mm) cc_final: 0.8397 (mt)
REVERT: A  276 ASN cc_start: 0.6779 (p0) cc_final: 0.6314 (m-40)
REVERT: C  295 LEU cc_start: 0.8700 (mt) cc_final: 0.8423 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1917
  time to fit residues: 44.2093
Evaluate side-chains
  119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 271 ASN
A 271 ASN
C 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.187414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.165435 restraints weight = 10862.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.169667 restraints weight = 6752.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.172722 restraints weight = 4677.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5227  Z= 0.190
  Angle     :  0.718   6.889   7021  Z= 0.399
  Chirality :  0.045   0.186    800
  Planarity :  0.005   0.051    823
  Dihedral  : 13.223  74.521    725
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.24 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.06 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.34), residues: 580
  helix:  1.46 (0.25), residues: 374
  sheet:  0.10 (1.03), residues: 35
  loop : -0.70 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 110 
 HIS   0.006   0.002   HIS B 213 
 PHE   0.025   0.002   PHE B  16 
 TYR   0.019   0.002   TYR B 127 
 ARG   0.006   0.001   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08416 (  299)
  hydrogen bonds       : angle       5.13988 (  870)
  metal coordination   : bond        0.00255 (    4)
  covalent geometry    : bond        0.00355 ( 5223)
  covalent geometry    : angle       0.71753 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 MET cc_start: 0.7428 (mmt) cc_final: 0.6801 (ptp)
REVERT: B   22 PHE cc_start: 0.7086 (m-80) cc_final: 0.6800 (m-80)
REVERT: B  136 LEU cc_start: 0.7424 (tp) cc_final: 0.6703 (mp)
REVERT: B  168 GLN cc_start: 0.6752 (mp10) cc_final: 0.6211 (mm-40)
REVERT: B  240 ASP cc_start: 0.8437 (m-30) cc_final: 0.8046 (t0)
REVERT: A  122 LEU cc_start: 0.8400 (mt) cc_final: 0.8151 (tp)
REVERT: A  141 ASN cc_start: 0.7719 (m-40) cc_final: 0.7287 (p0)
REVERT: A  194 ARG cc_start: 0.6956 (ptt180) cc_final: 0.6646 (ptt180)
REVERT: C  295 LEU cc_start: 0.8544 (mt) cc_final: 0.7847 (tt)
  outliers start: 17
  outliers final: 8
  residues processed: 162
  average time/residue: 0.1500
  time to fit residues: 31.2715
Evaluate side-chains
  123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  328 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0370
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.7258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.185595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.163946 restraints weight = 10288.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.168395 restraints weight = 6486.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.171599 restraints weight = 4453.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5227  Z= 0.155
  Angle     :  0.647  11.692   7021  Z= 0.351
  Chirality :  0.043   0.211    800
  Planarity :  0.004   0.051    823
  Dihedral  : 11.944  87.386    725
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.60 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.34), residues: 580
  helix:  1.67 (0.25), residues: 374
  sheet: -0.23 (1.01), residues: 37
  loop : -0.93 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.020   0.002   PHE B  16 
 TYR   0.028   0.002   TYR A 186 
 ARG   0.005   0.001   ARG B 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07084 (  299)
  hydrogen bonds       : angle       4.72306 (  870)
  metal coordination   : bond        0.00168 (    4)
  covalent geometry    : bond        0.00295 ( 5223)
  covalent geometry    : angle       0.64702 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 MET cc_start: 0.7230 (mmt) cc_final: 0.7013 (ptm)
REVERT: B   22 PHE cc_start: 0.7100 (m-80) cc_final: 0.6788 (m-80)
REVERT: B  136 LEU cc_start: 0.7561 (tp) cc_final: 0.7201 (mp)
REVERT: B  240 ASP cc_start: 0.8494 (m-30) cc_final: 0.8107 (t0)
REVERT: B  266 MET cc_start: 0.7010 (tpt) cc_final: 0.6690 (tpt)
REVERT: A   22 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7789 (t80)
REVERT: A  122 LEU cc_start: 0.8493 (mt) cc_final: 0.8279 (tp)
REVERT: A  141 ASN cc_start: 0.7658 (m-40) cc_final: 0.7328 (p0)
REVERT: A  165 GLU cc_start: 0.6927 (pm20) cc_final: 0.6645 (pt0)
REVERT: A  186 TYR cc_start: 0.7557 (m-10) cc_final: 0.7329 (m-80)
REVERT: A  246 ASP cc_start: 0.7209 (m-30) cc_final: 0.6998 (t0)
REVERT: C  300 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: C  330 MET cc_start: 0.4496 (tpp) cc_final: 0.3434 (tmm)
  outliers start: 20
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1508
  time to fit residues: 28.5056
Evaluate side-chains
  132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  328 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.183688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.162331 restraints weight = 10360.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.166610 restraints weight = 6541.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.169867 restraints weight = 4527.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.5459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5227  Z= 0.159
  Angle     :  0.630   9.092   7021  Z= 0.343
  Chirality :  0.043   0.190    800
  Planarity :  0.004   0.051    823
  Dihedral  : 11.235  83.033    725
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 16.31 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.34), residues: 580
  helix:  1.74 (0.26), residues: 374
  sheet: -0.69 (0.97), residues: 36
  loop : -1.24 (0.43), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 201 
 PHE   0.021   0.002   PHE A 173 
 TYR   0.024   0.002   TYR B 127 
 ARG   0.004   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06440 (  299)
  hydrogen bonds       : angle       4.71043 (  870)
  metal coordination   : bond        0.00503 (    4)
  covalent geometry    : bond        0.00319 ( 5223)
  covalent geometry    : angle       0.62971 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.605 
Fit side-chains
REVERT: B   22 PHE cc_start: 0.7005 (m-80) cc_final: 0.6690 (m-80)
REVERT: B  136 LEU cc_start: 0.7515 (tp) cc_final: 0.6670 (mp)
REVERT: B  240 ASP cc_start: 0.8559 (m-30) cc_final: 0.8245 (t0)
REVERT: B  266 MET cc_start: 0.6995 (tpt) cc_final: 0.6696 (tpt)
REVERT: A   22 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7833 (t80)
REVERT: A  122 LEU cc_start: 0.8494 (mt) cc_final: 0.8279 (tp)
REVERT: A  123 LYS cc_start: 0.7951 (tttt) cc_final: 0.7600 (pttm)
REVERT: A  165 GLU cc_start: 0.6881 (pm20) cc_final: 0.6599 (pt0)
REVERT: A  224 MET cc_start: 0.7294 (mmm) cc_final: 0.7069 (mmm)
REVERT: A  246 ASP cc_start: 0.7462 (m-30) cc_final: 0.7190 (t0)
REVERT: C  300 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8078 (tm-30)
REVERT: C  325 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8424 (tm-30)
  outliers start: 25
  outliers final: 18
  residues processed: 139
  average time/residue: 0.1525
  time to fit residues: 27.7112
Evaluate side-chains
  131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0270
   chunk 10 optimal weight:    0.0980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.5438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.187734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.165850 restraints weight = 10079.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.170578 restraints weight = 6202.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.173894 restraints weight = 4208.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6732
moved from start:          0.6004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5227  Z= 0.133
  Angle     :  0.596   9.060   7021  Z= 0.321
  Chirality :  0.042   0.192    800
  Planarity :  0.004   0.050    823
  Dihedral  : 10.362  71.547    725
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.97 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.34), residues: 580
  helix:  1.84 (0.26), residues: 374
  sheet: -0.78 (0.96), residues: 36
  loop : -1.35 (0.43), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.024   0.001   PHE C 328 
 TYR   0.020   0.002   TYR A 186 
 ARG   0.007   0.001   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05553 (  299)
  hydrogen bonds       : angle       4.54539 (  870)
  metal coordination   : bond        0.00213 (    4)
  covalent geometry    : bond        0.00251 ( 5223)
  covalent geometry    : angle       0.59634 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 PHE cc_start: 0.7044 (m-80) cc_final: 0.6710 (m-80)
REVERT: B  136 LEU cc_start: 0.7475 (tp) cc_final: 0.7025 (mp)
REVERT: B  203 TYR cc_start: 0.6943 (t80) cc_final: 0.6642 (t80)
REVERT: B  240 ASP cc_start: 0.8638 (m-30) cc_final: 0.8226 (t0)
REVERT: B  319 PHE cc_start: 0.7585 (t80) cc_final: 0.7381 (t80)
REVERT: A  100 ASP cc_start: 0.4365 (m-30) cc_final: 0.3878 (t0)
REVERT: A  122 LEU cc_start: 0.8500 (mt) cc_final: 0.8277 (tp)
REVERT: A  142 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7508 (mt-10)
REVERT: A  165 GLU cc_start: 0.6996 (pm20) cc_final: 0.6714 (pt0)
REVERT: A  246 ASP cc_start: 0.7218 (m-30) cc_final: 0.6943 (t0)
REVERT: A  271 ASN cc_start: 0.6345 (m-40) cc_final: 0.5986 (p0)
REVERT: C  300 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8043 (tm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 134
  average time/residue: 0.1640
  time to fit residues: 28.8451
Evaluate side-chains
  124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0060
   chunk 52 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0170
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.9636

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.188791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.166832 restraints weight = 11046.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.171256 restraints weight = 6951.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.174347 restraints weight = 4822.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.6352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5227  Z= 0.135
  Angle     :  0.597  13.573   7021  Z= 0.319
  Chirality :  0.041   0.179    800
  Planarity :  0.004   0.052    823
  Dihedral  : 10.004  69.610    725
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.10 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.35), residues: 580
  helix:  1.87 (0.26), residues: 373
  sheet: -0.56 (0.97), residues: 36
  loop : -1.25 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.025   0.001   PHE C 328 
 TYR   0.017   0.002   TYR A 261 
 ARG   0.005   0.001   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05478 (  299)
  hydrogen bonds       : angle       4.51591 (  870)
  metal coordination   : bond        0.00355 (    4)
  covalent geometry    : bond        0.00269 ( 5223)
  covalent geometry    : angle       0.59701 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 LEU cc_start: 0.7328 (tp) cc_final: 0.7057 (mp)
REVERT: B  162 ARG cc_start: 0.6208 (mtt180) cc_final: 0.5938 (ttm170)
REVERT: B  240 ASP cc_start: 0.8505 (m-30) cc_final: 0.8178 (t0)
REVERT: A  100 ASP cc_start: 0.4461 (m-30) cc_final: 0.3895 (t0)
REVERT: A  122 LEU cc_start: 0.8529 (mt) cc_final: 0.8277 (tp)
REVERT: A  142 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: A  224 MET cc_start: 0.7533 (mmm) cc_final: 0.7254 (mmm)
REVERT: A  246 ASP cc_start: 0.7234 (m-30) cc_final: 0.6940 (t0)
REVERT: C  300 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8229 (tm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 133
  average time/residue: 0.1468
  time to fit residues: 25.9704
Evaluate side-chains
  130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 PHE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0870
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.8760

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
A 271 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.188438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.167072 restraints weight = 10260.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.171409 restraints weight = 6464.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.174604 restraints weight = 4501.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.6650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5227  Z= 0.128
  Angle     :  0.608  13.893   7021  Z= 0.317
  Chirality :  0.041   0.179    800
  Planarity :  0.004   0.051    823
  Dihedral  :  9.761  75.007    725
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.70 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.35), residues: 580
  helix:  1.95 (0.26), residues: 373
  sheet: -0.70 (0.97), residues: 36
  loop : -1.27 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.024   0.001   PHE B 151 
 TYR   0.017   0.002   TYR A 261 
 ARG   0.005   0.001   ARG A 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05125 (  299)
  hydrogen bonds       : angle       4.39840 (  870)
  metal coordination   : bond        0.00335 (    4)
  covalent geometry    : bond        0.00258 ( 5223)
  covalent geometry    : angle       0.60778 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 LEU cc_start: 0.7292 (tp) cc_final: 0.6878 (mp)
REVERT: B  186 TYR cc_start: 0.7508 (m-80) cc_final: 0.7047 (m-80)
REVERT: B  240 ASP cc_start: 0.8619 (m-30) cc_final: 0.8281 (t0)
REVERT: B  255 LYS cc_start: 0.8630 (mttt) cc_final: 0.8062 (mmtt)
REVERT: A  122 LEU cc_start: 0.8526 (mt) cc_final: 0.8249 (tp)
REVERT: A  134 GLN cc_start: 0.8047 (mm110) cc_final: 0.7839 (mm-40)
REVERT: A  142 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: A  165 GLU cc_start: 0.7144 (pm20) cc_final: 0.6658 (pt0)
REVERT: A  168 GLN cc_start: 0.6295 (pm20) cc_final: 0.6068 (pp30)
REVERT: A  224 MET cc_start: 0.7563 (mmm) cc_final: 0.7347 (mmm)
REVERT: A  246 ASP cc_start: 0.7196 (m-30) cc_final: 0.6889 (t0)
REVERT: A  280 LEU cc_start: 0.7855 (mt) cc_final: 0.7600 (pp)
REVERT: C  300 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: C  330 MET cc_start: 0.4298 (tmm) cc_final: 0.3489 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 134
  average time/residue: 0.1585
  time to fit residues: 27.5339
Evaluate side-chains
  129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0980
   chunk 26 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.191173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.169455 restraints weight = 11048.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.173833 restraints weight = 6915.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.176972 restraints weight = 4769.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.6884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5227  Z= 0.125
  Angle     :  0.605  13.789   7021  Z= 0.314
  Chirality :  0.041   0.173    800
  Planarity :  0.004   0.051    823
  Dihedral  :  9.517  79.185    725
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.94 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.36), residues: 580
  helix:  1.94 (0.26), residues: 373
  sheet: -0.78 (0.99), residues: 36
  loop : -1.29 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 174 
 HIS   0.005   0.001   HIS B 213 
 PHE   0.021   0.001   PHE B 151 
 TYR   0.015   0.001   TYR A 261 
 ARG   0.008   0.001   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04933 (  299)
  hydrogen bonds       : angle       4.33482 (  870)
  metal coordination   : bond        0.00249 (    4)
  covalent geometry    : bond        0.00248 ( 5223)
  covalent geometry    : angle       0.60497 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7508 (mp)
REVERT: B  136 LEU cc_start: 0.7267 (tp) cc_final: 0.6783 (mp)
REVERT: B  162 ARG cc_start: 0.6248 (mtt180) cc_final: 0.6035 (ttm170)
REVERT: B  186 TYR cc_start: 0.7461 (m-80) cc_final: 0.7069 (m-80)
REVERT: B  240 ASP cc_start: 0.8549 (m-30) cc_final: 0.8265 (t0)
REVERT: A  106 CYS cc_start: 0.7432 (m) cc_final: 0.7062 (m)
REVERT: A  122 LEU cc_start: 0.8578 (mt) cc_final: 0.8291 (tp)
REVERT: A  211 THR cc_start: 0.8274 (p) cc_final: 0.7964 (p)
REVERT: A  246 ASP cc_start: 0.7122 (m-30) cc_final: 0.6802 (t0)
REVERT: A  271 ASN cc_start: 0.6292 (m-40) cc_final: 0.6042 (p0)
REVERT: A  280 LEU cc_start: 0.7796 (mt) cc_final: 0.7545 (pp)
REVERT: C  300 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: C  322 MET cc_start: 0.7182 (ttp) cc_final: 0.6639 (ttp)
REVERT: C  325 GLN cc_start: 0.8363 (pp30) cc_final: 0.8063 (pp30)
REVERT: C  330 MET cc_start: 0.4427 (tmm) cc_final: 0.3509 (tpt)
  outliers start: 15
  outliers final: 11
  residues processed: 141
  average time/residue: 0.1558
  time to fit residues: 29.1389
Evaluate side-chains
  136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0570
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.190047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.168585 restraints weight = 11137.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.173070 restraints weight = 6911.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.176091 restraints weight = 4740.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.7038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5227  Z= 0.127
  Angle     :  0.606  11.000   7021  Z= 0.318
  Chirality :  0.042   0.178    800
  Planarity :  0.004   0.050    823
  Dihedral  :  9.492  83.351    725
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.82 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.35), residues: 580
  helix:  1.93 (0.26), residues: 373
  sheet: -0.83 (0.99), residues: 36
  loop : -1.33 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 174 
 HIS   0.006   0.001   HIS B 213 
 PHE   0.023   0.001   PHE B 151 
 TYR   0.016   0.001   TYR A 261 
 ARG   0.004   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04851 (  299)
  hydrogen bonds       : angle       4.29046 (  870)
  metal coordination   : bond        0.00304 (    4)
  covalent geometry    : bond        0.00256 ( 5223)
  covalent geometry    : angle       0.60601 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7425 (mp)
REVERT: B  136 LEU cc_start: 0.7289 (tp) cc_final: 0.6615 (mp)
REVERT: B  186 TYR cc_start: 0.7460 (m-80) cc_final: 0.7122 (m-80)
REVERT: B  240 ASP cc_start: 0.8505 (m-30) cc_final: 0.8272 (t0)
REVERT: B  300 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6112 (pp20)
REVERT: A  106 CYS cc_start: 0.7400 (m) cc_final: 0.7049 (m)
REVERT: A  122 LEU cc_start: 0.8560 (mt) cc_final: 0.8265 (tp)
REVERT: A  165 GLU cc_start: 0.7076 (pm20) cc_final: 0.6707 (pm20)
REVERT: A  194 ARG cc_start: 0.6862 (ptt180) cc_final: 0.6640 (ptt-90)
REVERT: A  211 THR cc_start: 0.8298 (p) cc_final: 0.7984 (p)
REVERT: A  246 ASP cc_start: 0.7239 (m-30) cc_final: 0.6946 (t0)
REVERT: A  280 LEU cc_start: 0.7841 (mt) cc_final: 0.7563 (pp)
REVERT: C  300 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8369 (tm-30)
REVERT: C  330 MET cc_start: 0.4480 (tmm) cc_final: 0.3568 (tpt)
  outliers start: 17
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1425
  time to fit residues: 25.1269
Evaluate side-chains
  133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0870
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.190401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.168099 restraints weight = 10947.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.172452 restraints weight = 6829.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.175578 restraints weight = 4744.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.7203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5227  Z= 0.125
  Angle     :  0.597  10.965   7021  Z= 0.314
  Chirality :  0.042   0.184    800
  Planarity :  0.004   0.052    823
  Dihedral  :  9.394  86.153    725
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 25.18 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.35), residues: 580
  helix:  1.91 (0.26), residues: 375
  sheet: -0.62 (1.02), residues: 36
  loop : -1.56 (0.44), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.023   0.001   PHE B 151 
 TYR   0.019   0.001   TYR B 175 
 ARG   0.004   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  299)
  hydrogen bonds       : angle       4.25992 (  870)
  metal coordination   : bond        0.00218 (    4)
  covalent geometry    : bond        0.00254 ( 5223)
  covalent geometry    : angle       0.59675 ( 7021)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 PHE cc_start: 0.6999 (m-10) cc_final: 0.6682 (m-80)
REVERT: B   34 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7401 (mp)
REVERT: B  136 LEU cc_start: 0.7622 (tp) cc_final: 0.6403 (mp)
REVERT: B  162 ARG cc_start: 0.6210 (mtt180) cc_final: 0.5614 (ttt90)
REVERT: B  240 ASP cc_start: 0.8552 (m-30) cc_final: 0.8306 (t0)
REVERT: B  255 LYS cc_start: 0.8460 (mptt) cc_final: 0.8193 (mmtm)
REVERT: B  300 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6106 (pp20)
REVERT: A  106 CYS cc_start: 0.7370 (m) cc_final: 0.7052 (m)
REVERT: A  122 LEU cc_start: 0.8562 (mt) cc_final: 0.8282 (tp)
REVERT: A  211 THR cc_start: 0.8322 (p) cc_final: 0.8008 (p)
REVERT: A  246 ASP cc_start: 0.7191 (m-30) cc_final: 0.6873 (t0)
REVERT: A  280 LEU cc_start: 0.7813 (mt) cc_final: 0.7539 (pp)
REVERT: C  300 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: C  330 MET cc_start: 0.4528 (tmm) cc_final: 0.3595 (tpt)
  outliers start: 15
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1388
  time to fit residues: 24.3563
Evaluate side-chains
  131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  163 LYS
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.187757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.164938 restraints weight = 11206.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.169310 restraints weight = 6990.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.172607 restraints weight = 4851.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.7184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5227  Z= 0.135
  Angle     :  0.602  10.627   7021  Z= 0.322
  Chirality :  0.042   0.184    800
  Planarity :  0.004   0.049    823
  Dihedral  :  9.585  89.356    725
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 25.35 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.35), residues: 580
  helix:  1.87 (0.26), residues: 375
  sheet: -0.45 (0.99), residues: 37
  loop : -1.71 (0.44), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 174 
 HIS   0.005   0.001   HIS B 213 
 PHE   0.022   0.001   PHE B 151 
 TYR   0.019   0.002   TYR B 186 
 ARG   0.004   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  299)
  hydrogen bonds       : angle       4.30215 (  870)
  metal coordination   : bond        0.00418 (    4)
  covalent geometry    : bond        0.00282 ( 5223)
  covalent geometry    : angle       0.60188 ( 7021)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1925.05 seconds
wall clock time: 34 minutes 25.94 seconds (2065.94 seconds total)