Starting phenix.real_space_refine
on Wed Sep 17 09:58:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9euy_19989/09_2025/9euy_19989_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9euy_19989/09_2025/9euy_19989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9euy_19989/09_2025/9euy_19989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9euy_19989/09_2025/9euy_19989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9euy_19989/09_2025/9euy_19989_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9euy_19989/09_2025/9euy_19989_neut.cif"
  }
  resolution = 2.95
  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=  -0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4942      2.51       5
     N    1400      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 7846
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3880
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463}
    Chain: "B"
      Number of atoms: 3880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3880
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.43, per 1000 atoms: 0.31
  Number of scatterers: 7846
  At special positions: 0
  Unit cell: (85.284, 105.156, 119.232, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1466      8.00
     N    1400      7.00
     C    4942      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: 0.70
  Conformation dependent library (CDL) restraints added in 557.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      42.4% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 44 through 50
    Processing helix  chain 'A' and resid 60 through 78
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 116 through 134
      removed outlier: 3.830A  pdb=" N   ILE A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 139 through 156
    Processing helix  chain 'A' and resid 191 through 195
    Processing helix  chain 'A' and resid 196 through 206
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 285 through 332
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.627A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 345 through 350'
    Processing helix  chain 'A' and resid 370 through 382
    Processing helix  chain 'A' and resid 430 through 437
      removed outlier: 3.934A  pdb=" N   TRP A 437 " --> pdb=" O   HIS A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 468
    Processing helix  chain 'A' and resid 475 through 492
    Processing helix  chain 'B' and resid 11 through 15
    Processing helix  chain 'B' and resid 44 through 50
    Processing helix  chain 'B' and resid 64 through 77
      removed outlier: 4.351A  pdb=" N   VAL B  68 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 134
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 139 through 156
      removed outlier: 3.550A  pdb=" N   ASP B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 195
    Processing helix  chain 'B' and resid 196 through 206
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 285 through 332
      removed outlier: 4.018A  pdb=" N   ARG B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 340
    Processing helix  chain 'B' and resid 345 through 349
    Processing helix  chain 'B' and resid 370 through 382
    Processing helix  chain 'B' and resid 418 through 421
      removed outlier: 4.045A  pdb=" N   SER B 421 " --> pdb=" O   ARG B 418 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 418 through 421'
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 4.578A  pdb=" N   TRP B 437 " --> pdb=" O   HIS B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 467
    Processing helix  chain 'B' and resid 475 through 490
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 3.548A  pdb=" N   ALA A  40 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU A  29 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190
      removed outlier: 5.916A  pdb=" N   VAL A 173 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ARG A 164 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 175 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366
      removed outlier: 6.196A  pdb=" N   GLY A 422 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 3.561A  pdb=" N   ALA B  40 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU B  29 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 190
      removed outlier: 5.719A  pdb=" N   VAL B 173 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ARG B 164 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA B 175 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   VAL B 266 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 362 through 366
      removed outlier: 7.162A  pdb=" N   ILE B 424 " --> pdb=" O   ARG B 415 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ARG B 415 " --> pdb=" O   ILE B 424 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   TRP B 426 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ALA B 413 " --> pdb=" O   TRP B 426 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ARG B 428 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   VAL B 411 " --> pdb=" O   ARG B 428 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1185 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: 1.35

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1410
        1.32 -     1.44: 2081
        1.44 -     1.57: 4475
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 8028
  Sorted by residual:
  bond pdb=" CB  MET B 154 "
       pdb=" CG  MET B 154 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.33e+00
  bond pdb=" CB  MET A 154 "
       pdb=" CG  MET A 154 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CB  ILE B 447 "
       pdb=" CG2 ILE B 447 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG1 ILE A 294 "
       pdb=" CD1 ILE A 294 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.11e+00
  bond pdb=" CG1 ILE B 294 "
       pdb=" CD1 ILE B 294 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.93e-01
  ... (remaining 8023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 10415
        1.62 -     3.24: 430
        3.24 -     4.86: 54
        4.86 -     6.49: 9
        6.49 -     8.11: 4
  Bond angle restraints: 10912
  Sorted by residual:
  angle pdb=" CD  ARG A 453 "
        pdb=" NE  ARG A 453 "
        pdb=" CZ  ARG A 453 "
      ideal   model   delta    sigma   weight residual
     124.40  129.06   -4.66 1.40e+00 5.10e-01 1.11e+01
  angle pdb=" CB  ARG B 453 "
        pdb=" CG  ARG B 453 "
        pdb=" CD  ARG B 453 "
      ideal   model   delta    sigma   weight residual
     111.30  118.61   -7.31 2.30e+00 1.89e-01 1.01e+01
  angle pdb=" N   PRO B 452 "
        pdb=" CA  PRO B 452 "
        pdb=" C   PRO B 452 "
      ideal   model   delta    sigma   weight residual
     113.86  117.57   -3.71 1.25e+00 6.40e-01 8.83e+00
  angle pdb=" CG  ARG A 453 "
        pdb=" CD  ARG A 453 "
        pdb=" NE  ARG A 453 "
      ideal   model   delta    sigma   weight residual
     112.00  118.12   -6.12 2.20e+00 2.07e-01 7.75e+00
  angle pdb=" CB  MET A 154 "
        pdb=" CG  MET A 154 "
        pdb=" SD  MET A 154 "
      ideal   model   delta    sigma   weight residual
     112.70  104.59    8.11 3.00e+00 1.11e-01 7.30e+00
  ... (remaining 10907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 4513
       17.15 -    34.31: 239
       34.31 -    51.46: 51
       51.46 -    68.61: 14
       68.61 -    85.76: 9
  Dihedral angle restraints: 4826
    sinusoidal: 1994
      harmonic: 2832
  Sorted by residual:
  dihedral pdb=" CG  ARG A 453 "
           pdb=" CD  ARG A 453 "
           pdb=" NE  ARG A 453 "
           pdb=" CZ  ARG A 453 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00    5.38   84.62     2      1.50e+01 4.44e-03 2.11e+01
  dihedral pdb=" CA  ASP B  96 "
           pdb=" CB  ASP B  96 "
           pdb=" CG  ASP B  96 "
           pdb=" OD1 ASP B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.23   53.23     1      2.00e+01 2.50e-03 9.63e+00
  dihedral pdb=" CG  ARG A 201 "
           pdb=" CD  ARG A 201 "
           pdb=" NE  ARG A 201 "
           pdb=" CZ  ARG A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.08   42.08     2      1.50e+01 4.44e-03 9.58e+00
  ... (remaining 4823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 785
       0.038 -    0.075: 257
       0.075 -    0.113: 93
       0.113 -    0.150: 48
       0.150 -    0.188: 5
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" CA  PRO B 452 "
            pdb=" N   PRO B 452 "
            pdb=" C   PRO B 452 "
            pdb=" CB  PRO B 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CA  PRO A 452 "
            pdb=" N   PRO A 452 "
            pdb=" C   PRO A 452 "
            pdb=" CB  PRO A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  ILE A 264 "
            pdb=" N   ILE A 264 "
            pdb=" C   ILE A 264 "
            pdb=" CB  ILE A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1185 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 152 "    0.236 9.50e-02 1.11e+02   1.06e-01 8.43e+00
        pdb=" NE  ARG B 152 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 152 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 152 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 152 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 434 "    0.212 9.50e-02 1.11e+02   9.57e-02 7.46e+00
        pdb=" NE  ARG B 434 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 434 "    0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 434 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 434 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 152 "   -0.211 9.50e-02 1.11e+02   9.49e-02 6.69e+00
        pdb=" NE  ARG A 152 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 152 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 152 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 152 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2280
        2.83 -     3.35: 7229
        3.35 -     3.86: 12967
        3.86 -     4.38: 15202
        4.38 -     4.90: 26273
  Nonbonded interactions: 63951
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 178 "
            pdb=" O   LEU A 182 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NH1 ARG B 178 "
            pdb=" O   LEU B 182 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" NH1 ARG A 322 "
            pdb=" OD2 ASP A 488 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OG  SER A 399 "
            pdb=" OD1 ASP A 401 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" OD1 ASP B 234 "
            pdb=" OG  SER B 236 "
     model   vdw
     2.411 3.040
  ... (remaining 63946 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.270
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.960
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:6.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8028  Z= 0.153
  Angle     :  0.735   8.108  10912  Z= 0.419
  Chirality :  0.048   0.188   1188
  Planarity :  0.010   0.106   1434
  Dihedral  : 11.993  85.765   3002
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.03 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.41 (0.26), residues: 980
  helix:  0.76 (0.26), residues: 352
  sheet:  0.42 (0.40), residues: 166
  loop : -0.03 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.003   ARG B 434 
 TYR   0.017   0.004   TYR B 163 
 PHE   0.020   0.003   PHE A 274 
 TRP   0.025   0.003   TRP A  82 
 HIS   0.008   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8028)
  covalent geometry    : angle       0.73505 (10912)
  hydrogen bonds       : bond        0.14118 (  423)
  hydrogen bonds       : angle       7.11464 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ASP cc_start: 0.7286 (t70) cc_final: 0.6877 (p0)
REVERT: A  394 ASN cc_start: 0.8018 (t0) cc_final: 0.7630 (t160)
REVERT: A  395 TRP cc_start: 0.7284 (t-100) cc_final: 0.7045 (t60)
REVERT: A  470 HIS cc_start: 0.7316 (m90) cc_final: 0.6841 (m90)
REVERT: B  228 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7259 (mm-30)
REVERT: B  314 LEU cc_start: 0.7674 (mt) cc_final: 0.7435 (mp)
REVERT: B  353 ASP cc_start: 0.7189 (m-30) cc_final: 0.6969 (m-30)
REVERT: B  430 GLU cc_start: 0.3794 (tt0) cc_final: 0.3572 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 0.6508
  time to fit residues: 123.1450
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  79 ASN
A 137 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 HIS
B 137 HIS
B 278 HIS
B 391 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.189466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.140619 restraints weight = 9302.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.04
r_work: 0.3435 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8028  Z= 0.167
  Angle     :  0.590   7.944  10912  Z= 0.314
  Chirality :  0.046   0.174   1188
  Planarity :  0.005   0.038   1434
  Dihedral  :  6.956  88.338   1142
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  :  9.55 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.38 (0.27), residues: 980
  helix:  1.74 (0.27), residues: 360
  sheet:  0.60 (0.41), residues: 162
  loop :  0.51 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  89 
 TYR   0.010   0.002   TYR B 163 
 PHE   0.014   0.002   PHE B 295 
 TRP   0.016   0.002   TRP A  82 
 HIS   0.005   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8028)
  covalent geometry    : angle       0.58966 (10912)
  hydrogen bonds       : bond        0.04143 (  423)
  hydrogen bonds       : angle       5.58201 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.8783 (tt0) cc_final: 0.8577 (tt0)
REVERT: A  394 ASN cc_start: 0.8054 (t0) cc_final: 0.7649 (t160)
REVERT: A  395 TRP cc_start: 0.7250 (t-100) cc_final: 0.6805 (t60)
REVERT: A  440 LYS cc_start: 0.7672 (mttt) cc_final: 0.7396 (mtpt)
REVERT: A  465 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7163 (tt0)
REVERT: A  470 HIS cc_start: 0.7539 (m90) cc_final: 0.7145 (m170)
REVERT: B   43 GLU cc_start: 0.8132 (tt0) cc_final: 0.7760 (tp30)
REVERT: B   48 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7252 (tt)
REVERT: B  220 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7138 (mmt180)
REVERT: B  228 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7351 (mm-30)
REVERT: B  353 ASP cc_start: 0.6957 (m-30) cc_final: 0.6585 (m-30)
  outliers start: 28
  outliers final: 12
  residues processed: 134
  average time/residue: 0.5966
  time to fit residues: 84.6088
Evaluate side-chains
  114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 87 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0970
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.190124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135042 restraints weight = 9305.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.31
r_work: 0.3445 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8028  Z= 0.135
  Angle     :  0.520   5.340  10912  Z= 0.276
  Chirality :  0.044   0.164   1188
  Planarity :  0.004   0.042   1434
  Dihedral  :  6.772  87.758   1142
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.58 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.54 (0.27), residues: 980
  helix:  2.10 (0.26), residues: 360
  sheet:  0.58 (0.42), residues: 162
  loop :  0.43 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  33 
 TYR   0.010   0.001   TYR A  58 
 PHE   0.012   0.002   PHE B 295 
 TRP   0.013   0.001   TRP B 423 
 HIS   0.004   0.001   HIS A 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8028)
  covalent geometry    : angle       0.51955 (10912)
  hydrogen bonds       : bond        0.03709 (  423)
  hydrogen bonds       : angle       5.22761 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7693 (mp)
REVERT: A  139 ASP cc_start: 0.7404 (t70) cc_final: 0.7165 (OUTLIER)
REVERT: A  219 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.5960 (mmt)
REVERT: A  395 TRP cc_start: 0.7259 (t-100) cc_final: 0.6765 (t60)
REVERT: A  440 LYS cc_start: 0.7630 (mttt) cc_final: 0.7366 (mtpt)
REVERT: A  465 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7178 (tt0)
REVERT: B   43 GLU cc_start: 0.8163 (tt0) cc_final: 0.7780 (tp30)
REVERT: B   48 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7217 (tt)
REVERT: B  135 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8231 (mp10)
REVERT: B  220 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7149 (mmt180)
REVERT: B  228 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7450 (mm-30)
REVERT: B  353 ASP cc_start: 0.7071 (m-30) cc_final: 0.6609 (m-30)
  outliers start: 31
  outliers final: 13
  residues processed: 138
  average time/residue: 0.5231
  time to fit residues: 77.0018
Evaluate side-chains
  119 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 77 optimal weight:    0.1980
   chunk 91 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0010
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 206 ASN
A 226 ASN
A 394 ASN
B 308 GLN
B 391 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.190382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140884 restraints weight = 9432.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.19
r_work: 0.3454 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8028  Z= 0.121
  Angle     :  0.517  10.093  10912  Z= 0.268
  Chirality :  0.044   0.167   1188
  Planarity :  0.004   0.039   1434
  Dihedral  :  6.654  83.635   1142
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.48 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.67 (0.27), residues: 980
  helix:  2.34 (0.26), residues: 360
  sheet:  0.55 (0.43), residues: 162
  loop :  0.42 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 457 
 TYR   0.009   0.001   TYR B 286 
 PHE   0.010   0.001   PHE B 295 
 TRP   0.013   0.001   TRP A 426 
 HIS   0.008   0.001   HIS B 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8028)
  covalent geometry    : angle       0.51733 (10912)
  hydrogen bonds       : bond        0.03497 (  423)
  hydrogen bonds       : angle       5.05609 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7602 (mp)
REVERT: A  219 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6008 (mmt)
REVERT: A  395 TRP cc_start: 0.7092 (t-100) cc_final: 0.6497 (t60)
REVERT: A  440 LYS cc_start: 0.7754 (mttt) cc_final: 0.7421 (mtpt)
REVERT: A  465 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7164 (tt0)
REVERT: B   43 GLU cc_start: 0.8090 (tt0) cc_final: 0.7721 (tp30)
REVERT: B   88 THR cc_start: 0.8738 (t) cc_final: 0.8429 (p)
REVERT: B  135 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8233 (mp10)
REVERT: B  220 ARG cc_start: 0.7635 (mtm180) cc_final: 0.7085 (mmt180)
REVERT: B  228 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7386 (mm-30)
REVERT: B  353 ASP cc_start: 0.7149 (m-30) cc_final: 0.6686 (m-30)
  outliers start: 33
  outliers final: 14
  residues processed: 122
  average time/residue: 0.5208
  time to fit residues: 67.6444
Evaluate side-chains
  110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0370
   chunk 75 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0070
   chunk 79 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.192463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.135809 restraints weight = 9206.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.36
r_work: 0.3476 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8028  Z= 0.110
  Angle     :  0.519  16.031  10912  Z= 0.263
  Chirality :  0.043   0.159   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.565  80.529   1142
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 15.27 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.77 (0.27), residues: 980
  helix:  2.43 (0.27), residues: 360
  sheet:  0.63 (0.44), residues: 162
  loop :  0.46 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 328 
 TYR   0.010   0.001   TYR B 286 
 PHE   0.009   0.001   PHE B 295 
 TRP   0.012   0.001   TRP A 426 
 HIS   0.009   0.001   HIS B 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8028)
  covalent geometry    : angle       0.51898 (10912)
  hydrogen bonds       : bond        0.03381 (  423)
  hydrogen bonds       : angle       4.98101 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7648 (mp)
REVERT: A  395 TRP cc_start: 0.7097 (t-100) cc_final: 0.6509 (t60)
REVERT: A  440 LYS cc_start: 0.7818 (mttt) cc_final: 0.7495 (mtpt)
REVERT: A  465 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7294 (tt0)
REVERT: B   43 GLU cc_start: 0.8111 (tt0) cc_final: 0.7729 (tp30)
REVERT: B   88 THR cc_start: 0.8675 (t) cc_final: 0.8391 (p)
REVERT: B  135 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8264 (mp10)
REVERT: B  220 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7229 (mmt180)
REVERT: B  353 ASP cc_start: 0.7315 (m-30) cc_final: 0.6876 (m-30)
REVERT: B  443 LYS cc_start: 0.7121 (mmtm) cc_final: 0.6777 (mptt)
REVERT: B  485 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (tt)
  outliers start: 28
  outliers final: 16
  residues processed: 116
  average time/residue: 0.5708
  time to fit residues: 70.4344
Evaluate side-chains
  111 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 226 ASN
B 308 GLN
B 391 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.191339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140876 restraints weight = 9230.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.16
r_work: 0.3470 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8028  Z= 0.141
  Angle     :  0.531  12.519  10912  Z= 0.271
  Chirality :  0.044   0.162   1188
  Planarity :  0.004   0.036   1434
  Dihedral  :  6.524  76.223   1142
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 15.87 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.70 (0.27), residues: 980
  helix:  2.41 (0.27), residues: 360
  sheet:  0.60 (0.44), residues: 162
  loop :  0.37 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 113 
 TYR   0.010   0.001   TYR B 286 
 PHE   0.011   0.001   PHE B 295 
 TRP   0.011   0.001   TRP A 426 
 HIS   0.006   0.001   HIS B 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8028)
  covalent geometry    : angle       0.53104 (10912)
  hydrogen bonds       : bond        0.03494 (  423)
  hydrogen bonds       : angle       4.99953 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 97
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: A   46 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7567 (tp40)
REVERT: A  219 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5938 (mmt)
REVERT: A  395 TRP cc_start: 0.7112 (t-100) cc_final: 0.6541 (t60)
REVERT: A  465 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7384 (tt0)
REVERT: B   37 MET cc_start: 0.7733 (ttm) cc_final: 0.7356 (ttt)
REVERT: B   43 GLU cc_start: 0.8101 (tt0) cc_final: 0.7716 (tp30)
REVERT: B   88 THR cc_start: 0.8661 (t) cc_final: 0.8391 (p)
REVERT: B  135 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8239 (mp10)
REVERT: B  220 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7202 (mmt180)
REVERT: B  353 ASP cc_start: 0.7374 (m-30) cc_final: 0.6945 (m-30)
REVERT: B  443 LYS cc_start: 0.7062 (mmtm) cc_final: 0.6763 (mptt)
  outliers start: 33
  outliers final: 17
  residues processed: 120
  average time/residue: 0.5466
  time to fit residues: 69.9369
Evaluate side-chains
  118 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0870
   chunk 46 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 HIS ** 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 = 0.4243 r_free = 0.4243 target = 0.191548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.141310 restraints weight = 9219.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.18
r_work: 0.3468 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8028  Z= 0.131
  Angle     :  0.520   9.183  10912  Z= 0.266
  Chirality :  0.043   0.174   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.480  71.900   1142
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.71 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.72 (0.27), residues: 980
  helix:  2.40 (0.27), residues: 360
  sheet:  0.65 (0.42), residues: 172
  loop :  0.39 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  33 
 TYR   0.010   0.001   TYR B 286 
 PHE   0.010   0.001   PHE B 295 
 TRP   0.010   0.001   TRP A 426 
 HIS   0.007   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8028)
  covalent geometry    : angle       0.51971 (10912)
  hydrogen bonds       : bond        0.03465 (  423)
  hydrogen bonds       : angle       4.94540 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7679 (mp)
REVERT: A   46 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7567 (tp40)
REVERT: A   73 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7157 (tm-30)
REVERT: A  219 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.5959 (mmt)
REVERT: A  395 TRP cc_start: 0.7032 (t-100) cc_final: 0.6532 (t60)
REVERT: A  465 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7352 (tt0)
REVERT: B   43 GLU cc_start: 0.8114 (tt0) cc_final: 0.7720 (tp30)
REVERT: B   88 THR cc_start: 0.8648 (t) cc_final: 0.8372 (p)
REVERT: B  220 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7217 (mmt180)
REVERT: B  353 ASP cc_start: 0.7397 (m-30) cc_final: 0.6976 (m-30)
REVERT: B  443 LYS cc_start: 0.7029 (mmtm) cc_final: 0.6675 (mptt)
  outliers start: 28
  outliers final: 16
  residues processed: 119
  average time/residue: 0.5614
  time to fit residues: 71.2153
Evaluate side-chains
  110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 226 ASN
A 277 HIS
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 308 GLN
B 391 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.189700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.131006 restraints weight = 9245.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.37
r_work: 0.3484 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8028  Z= 0.155
  Angle     :  0.555  16.318  10912  Z= 0.281
  Chirality :  0.044   0.193   1188
  Planarity :  0.004   0.036   1434
  Dihedral  :  6.501  67.019   1142
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.95 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.54 (0.27), residues: 980
  helix:  2.24 (0.27), residues: 362
  sheet:  0.58 (0.42), residues: 172
  loop :  0.27 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 486 
 TYR   0.010   0.002   TYR B 286 
 PHE   0.011   0.001   PHE B 295 
 TRP   0.009   0.001   TRP A 423 
 HIS   0.007   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8028)
  covalent geometry    : angle       0.55522 (10912)
  hydrogen bonds       : bond        0.03553 (  423)
  hydrogen bonds       : angle       5.00738 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7722 (mp)
REVERT: A   46 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7633 (tp40)
REVERT: A   73 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7180 (tm-30)
REVERT: A  219 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.5880 (mmt)
REVERT: A  395 TRP cc_start: 0.7079 (t-100) cc_final: 0.6651 (t60)
REVERT: A  465 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7411 (tt0)
REVERT: B   43 GLU cc_start: 0.8116 (tt0) cc_final: 0.7782 (tp30)
REVERT: B   88 THR cc_start: 0.8669 (t) cc_final: 0.8422 (p)
REVERT: B  220 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7390 (mmt180)
REVERT: B  443 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6812 (mptt)
REVERT: B  485 LEU cc_start: 0.8403 (tt) cc_final: 0.8179 (tt)
  outliers start: 30
  outliers final: 15
  residues processed: 119
  average time/residue: 0.5475
  time to fit residues: 69.4678
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0370
   chunk 27 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.189560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.132364 restraints weight = 9211.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.30
r_work: 0.3495 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8028  Z= 0.138
  Angle     :  0.557  18.986  10912  Z= 0.279
  Chirality :  0.043   0.207   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.486  63.543   1142
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.78 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.57 (0.27), residues: 980
  helix:  2.29 (0.27), residues: 362
  sheet:  0.57 (0.42), residues: 172
  loop :  0.27 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  33 
 TYR   0.012   0.001   TYR A  58 
 PHE   0.010   0.001   PHE B 295 
 TRP   0.009   0.001   TRP A 423 
 HIS   0.006   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8028)
  covalent geometry    : angle       0.55734 (10912)
  hydrogen bonds       : bond        0.03499 (  423)
  hydrogen bonds       : angle       4.95339 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7650 (mp)
REVERT: A   46 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7609 (tp40)
REVERT: A   73 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7146 (tm-30)
REVERT: A  219 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.5906 (mmt)
REVERT: A  395 TRP cc_start: 0.7064 (t-100) cc_final: 0.6634 (t60)
REVERT: A  465 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7414 (tt0)
REVERT: B   43 GLU cc_start: 0.8095 (tt0) cc_final: 0.7753 (tp30)
REVERT: B   88 THR cc_start: 0.8659 (t) cc_final: 0.8413 (p)
REVERT: B  220 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7345 (mmt180)
REVERT: B  443 LYS cc_start: 0.7072 (mmtm) cc_final: 0.6787 (mptt)
REVERT: B  485 LEU cc_start: 0.8403 (tt) cc_final: 0.8184 (tt)
  outliers start: 23
  outliers final: 15
  residues processed: 110
  average time/residue: 0.5338
  time to fit residues: 62.7609
Evaluate side-chains
  109 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 28 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   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 226 ASN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 308 GLN
B 391 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.190613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.132312 restraints weight = 9241.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.36
r_work: 0.3498 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8028  Z= 0.132
  Angle     :  0.563  18.427  10912  Z= 0.282
  Chirality :  0.043   0.225   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.477  60.723   1142
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.14 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.59 (0.27), residues: 980
  helix:  2.29 (0.26), residues: 362
  sheet:  0.59 (0.42), residues: 172
  loop :  0.29 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  33 
 TYR   0.010   0.001   TYR B 286 
 PHE   0.009   0.001   PHE B 295 
 TRP   0.010   0.001   TRP A 423 
 HIS   0.009   0.001   HIS B 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8028)
  covalent geometry    : angle       0.56286 (10912)
  hydrogen bonds       : bond        0.03417 (  423)
  hydrogen bonds       : angle       4.88774 ( 1185)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7674 (mp)
REVERT: A   46 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7618 (tp40)
REVERT: A   73 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7109 (tm-30)
REVERT: A  219 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5911 (mmt)
REVERT: A  395 TRP cc_start: 0.7014 (t-100) cc_final: 0.6566 (t60)
REVERT: A  465 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7395 (tt0)
REVERT: B  220 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7374 (mmt180)
REVERT: B  443 LYS cc_start: 0.7015 (mmtm) cc_final: 0.6758 (mptt)
REVERT: B  485 LEU cc_start: 0.8417 (tt) cc_final: 0.8206 (tt)
  outliers start: 20
  outliers final: 15
  residues processed: 113
  average time/residue: 0.5308
  time to fit residues: 64.0631
Evaluate side-chains
  109 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.190662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.132055 restraints weight = 9221.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.34
r_work: 0.3484 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8028  Z= 0.159
  Angle     :  0.577  17.999  10912  Z= 0.288
  Chirality :  0.044   0.223   1188
  Planarity :  0.004   0.037   1434
  Dihedral  :  6.553  62.255   1142
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.26 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.51 (0.27), residues: 980
  helix:  2.24 (0.26), residues: 362
  sheet:  0.60 (0.42), residues: 172
  loop :  0.22 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A  33 
 TYR   0.012   0.002   TYR A  58 
 PHE   0.011   0.001   PHE B 295 
 TRP   0.013   0.001   TRP A 423 
 HIS   0.006   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8028)
  covalent geometry    : angle       0.57661 (10912)
  hydrogen bonds       : bond        0.03557 (  423)
  hydrogen bonds       : angle       4.91699 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3699.91 seconds
wall clock time: 63 minutes 42.54 seconds (3822.54 seconds total)