Starting phenix.real_space_refine
on Sat May 10 04:01:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnd_50590/05_2025/9fnd_50590.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnd_50590/05_2025/9fnd_50590.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fnd_50590/05_2025/9fnd_50590.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnd_50590/05_2025/9fnd_50590.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnd_50590/05_2025/9fnd_50590.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnd_50590/05_2025/9fnd_50590.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    3057      2.51       5
     N     889      2.21       5
     O     956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4914
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "X"
      Number of atoms: 2531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2531
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314}
    Chain: "Y"
      Number of atoms: 2383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2383
          Classifications: {'peptide': 317}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 296}
  Time building chain proxies: 3.14, per 1000 atoms: 0.64
  Number of scatterers: 4914
  At special positions: 0
  Unit cell: (97.65, 81.9, 108.675, 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      12     16.00
     O     956      8.00
     N     889      7.00
     C    3057      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: 1.04
  Conformation dependent library (CDL) restraints added in 555.6 milliseconds
  

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1206

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      43.0% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'X' and resid 4 through 18
    Processing helix  chain 'X' and resid 24 through 32
    Processing helix  chain 'X' and resid 40 through 58
    Processing helix  chain 'X' and resid 79 through 84
      removed outlier: 3.565A  pdb=" N   ALA X  84 " --> pdb=" O   ARG X  80 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 91 through 102
    Processing helix  chain 'X' and resid 107 through 125
      removed outlier: 3.840A  pdb=" N   GLY X 125 " --> pdb=" O   LEU X 121 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 150 through 163
    Processing helix  chain 'X' and resid 235 through 245
      removed outlier: 3.554A  pdb=" N   ALA X 245 " --> pdb=" O   ARG X 241 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 262 through 268
      removed outlier: 3.508A  pdb=" N   GLN X 268 " --> pdb=" O   ALA X 264 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 291 through 303
      removed outlier: 3.821A  pdb=" N   TYR X 302 " --> pdb=" O   GLU X 298 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY X 303 " --> pdb=" O   ILE X 299 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 311 through 327
    Processing helix  chain 'Y' and resid 3 through 21
      removed outlier: 4.588A  pdb=" N   VAL Y  15 " --> pdb=" O   LEU Y  11 " (cutoff:3.500A)
      Proline residue:  Y  16  - end of helix
    Processing helix  chain 'Y' and resid 26 through 34
    Processing helix  chain 'Y' and resid 36 through 49
      removed outlier: 3.554A  pdb=" N   MET Y  49 " --> pdb=" O   ASP Y  45 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 85 through 100
    Processing helix  chain 'Y' and resid 107 through 123
    Processing helix  chain 'Y' and resid 141 through 153
    Processing helix  chain 'Y' and resid 217 through 223
      removed outlier: 4.090A  pdb=" N   ALA Y 221 " --> pdb=" O   PRO Y 217 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 250 through 255
      removed outlier: 3.924A  pdb=" N   TYR Y 254 " --> pdb=" O   TRP Y 250 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR Y 255 " --> pdb=" O   MET Y 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 250 through 255'
    Processing helix  chain 'Y' and resid 276 through 288
      removed outlier: 3.832A  pdb=" N   PHE Y 287 " --> pdb=" O   PHE Y 283 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY Y 288 " --> pdb=" O   ILE Y 284 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 296 through 317
    Processing sheet with id=AA1, first strand: chain 'X' and resid 62 through 66
    Processing sheet with id=AA2, first strand: chain 'X' and resid 207 through 211
      removed outlier: 6.051A  pdb=" N   ARG X 194 " --> pdb=" O   THR X 190 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   THR X 190 " --> pdb=" O   ARG X 194 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   TYR X 196 " --> pdb=" O   VAL X 188 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   VAL X 188 " --> pdb=" O   TYR X 196 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   VAL X 198 " --> pdb=" O   TRP X 186 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'X' and resid 271 through 277
      removed outlier: 6.633A  pdb=" N   ARG X 254 " --> pdb=" O   LEU X 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 24 through 25
      removed outlier: 3.968A  pdb=" N   VAL Y  24 " --> pdb=" O   ILE Y  70 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 196 through 201
      removed outlier: 7.151A  pdb=" N   ASN Y 184 " --> pdb=" O   LEU Y 180 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU Y 180 " --> pdb=" O   ASN Y 184 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   TYR Y 186 " --> pdb=" O   VAL Y 178 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   VAL Y 178 " --> pdb=" O   TYR Y 186 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   GLU Y 188 " --> pdb=" O   ILE Y 176 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU Y 159 " --> pdb=" O   ASP Y 207 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ASP Y 207 " --> pdb=" O   GLU Y 159 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   TYR Y 161 " --> pdb=" O   ILE Y 205 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE Y 205 " --> pdb=" O   TYR Y 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 270 through 273
      removed outlier: 6.798A  pdb=" N   THR Y 241 " --> pdb=" O   LEU Y 294 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    699 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: 1.15

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1720
        1.34 -     1.46: 1006
        1.46 -     1.58: 2256
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 5002
  Sorted by residual:
  bond pdb=" C   PRO Y 218 "
       pdb=" N   PRO Y 219 "
    ideal  model  delta    sigma   weight residual
    1.329  1.341 -0.011 1.18e-02 7.18e+03 9.42e-01
  bond pdb=" CA  ASP Y 135 "
       pdb=" C   ASP Y 135 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.14e-02 7.69e+03 9.22e-01
  bond pdb=" CA  ASP Y 135 "
       pdb=" CB  ASP Y 135 "
    ideal  model  delta    sigma   weight residual
    1.529  1.515  0.014 1.54e-02 4.22e+03 8.66e-01
  bond pdb=" N   PRO Y 219 "
       pdb=" CA  PRO Y 219 "
    ideal  model  delta    sigma   weight residual
    1.465  1.482 -0.017 2.03e-02 2.43e+03 7.35e-01
  bond pdb=" CB  PRO X 221 "
       pdb=" CG  PRO X 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.527 -0.035 5.00e-02 4.00e+02 4.85e-01
  ... (remaining 4997 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 6613
        0.98 -     1.95: 151
        1.95 -     2.93: 36
        2.93 -     3.91: 15
        3.91 -     4.88: 5
  Bond angle restraints: 6820
  Sorted by residual:
  angle pdb=" N   PRO Y 218 "
        pdb=" CA  PRO Y 218 "
        pdb=" C   PRO Y 218 "
      ideal   model   delta    sigma   weight residual
     110.70  113.82   -3.12 1.22e+00 6.72e-01 6.53e+00
  angle pdb=" CA  PRO Y 218 "
        pdb=" C   PRO Y 218 "
        pdb=" N   PRO Y 219 "
      ideal   model   delta    sigma   weight residual
     117.93  120.45   -2.52 1.20e+00 6.94e-01 4.40e+00
  angle pdb=" N   PRO Y 219 "
        pdb=" CA  PRO Y 219 "
        pdb=" C   PRO Y 219 "
      ideal   model   delta    sigma   weight residual
     110.70  113.24   -2.54 1.22e+00 6.72e-01 4.35e+00
  angle pdb=" N   GLU Y 269 "
        pdb=" CA  GLU Y 269 "
        pdb=" C   GLU Y 269 "
      ideal   model   delta    sigma   weight residual
     109.65  112.79   -3.14 1.56e+00 4.11e-01 4.06e+00
  angle pdb=" CA  PRO Y 219 "
        pdb=" C   PRO Y 219 "
        pdb=" N   PRO Y 220 "
      ideal   model   delta    sigma   weight residual
     117.93  120.08   -2.15 1.20e+00 6.94e-01 3.22e+00
  ... (remaining 6815 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.44: 2829
       11.44 -    22.88: 158
       22.88 -    34.33: 36
       34.33 -    45.77: 15
       45.77 -    57.21: 2
  Dihedral angle restraints: 3040
    sinusoidal: 1173
      harmonic: 1867
  Sorted by residual:
  dihedral pdb=" CA  CYS Y 268 "
           pdb=" C   CYS Y 268 "
           pdb=" N   GLU Y 269 "
           pdb=" CA  GLU Y 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.40  -15.60     0      5.00e+00 4.00e-02 9.73e+00
  dihedral pdb=" CA  GLU X  63 "
           pdb=" CB  GLU X  63 "
           pdb=" CG  GLU X  63 "
           pdb=" CD  GLU X  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.79  -57.21     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CA  LEU Y  11 "
           pdb=" CB  LEU Y  11 "
           pdb=" CG  LEU Y  11 "
           pdb=" CD1 LEU Y  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.58   45.42     3      1.50e+01 4.44e-03 8.17e+00
  ... (remaining 3037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 491
       0.026 -    0.052: 177
       0.052 -    0.078: 64
       0.078 -    0.104: 42
       0.104 -    0.130: 16
  Chirality restraints: 790
  Sorted by residual:
  chirality pdb=" CA  ILE X 255 "
            pdb=" N   ILE X 255 "
            pdb=" C   ILE X 255 "
            pdb=" CB  ILE X 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  PRO Y  22 "
            pdb=" N   PRO Y  22 "
            pdb=" C   PRO Y  22 "
            pdb=" CB  PRO Y  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.53e-01
  chirality pdb=" CA  ILE Y  70 "
            pdb=" N   ILE Y  70 "
            pdb=" C   ILE Y  70 "
            pdb=" CB  ILE Y  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.40e-01
  ... (remaining 787 not shown)

  Planarity restraints: 904
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 219 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO Y 220 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 220 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 220 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 217 "    0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO Y 218 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 218 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 218 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 218 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO Y 219 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 219 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 219 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 901 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1285
        2.81 -     3.33: 4554
        3.33 -     3.86: 7777
        3.86 -     4.38: 8083
        4.38 -     4.90: 14578
  Nonbonded interactions: 36277
  Sorted by model distance:
  nonbonded pdb=" OG  SER X 272 "
            pdb=" OE1 GLU X 283 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OD1 ASN X  11 "
            pdb=" OH  TYR Y  55 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER Y   2 "
            pdb=" OG  SER Y   5 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" N   SER X 107 "
            pdb=" OE2 GLU X 150 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   VAL Y  66 "
            pdb=" OG1 THR Y  69 "
     model   vdw
     2.396 3.040
  ... (remaining 36272 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.890
  Find NCS groups from input model:        0.070
  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:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5002  Z= 0.091
  Angle     :  0.423   4.884   6820  Z= 0.229
  Chirality :  0.038   0.130    790
  Planarity :  0.004   0.047    904
  Dihedral  :  8.173  57.210   1834
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  4.34 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.57 (0.35), residues: 643
  helix:  2.84 (0.32), residues: 274
  sheet:  0.00 (0.47), residues: 111
  loop : -0.48 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Y 250 
 HIS   0.001   0.000   HIS X 325 
 PHE   0.007   0.001   PHE Y 231 
 TYR   0.006   0.001   TYR Y 186 
 ARG   0.002   0.000   ARG X 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11312 (  243)
  hydrogen bonds       : angle       4.70224 (  699)
  covalent geometry    : bond        0.00183 ( 5002)
  covalent geometry    : angle       0.42341 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.6563 (tpt) cc_final: 0.6105 (tpp)
REVERT: X   37 ASP cc_start: 0.6998 (m-30) cc_final: 0.6544 (t0)
REVERT: X   76 TYR cc_start: 0.7424 (m-10) cc_final: 0.7040 (m-10)
REVERT: X  106 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8001 (mm110)
REVERT: X  120 LYS cc_start: 0.8308 (mttp) cc_final: 0.8062 (mttt)
REVERT: X  168 PHE cc_start: 0.8517 (p90) cc_final: 0.8063 (p90)
REVERT: X  274 PRO cc_start: 0.6789 (Cg_exo) cc_final: 0.5881 (Cg_endo)
REVERT: X  298 GLU cc_start: 0.9194 (tt0) cc_final: 0.8957 (mt-10)
REVERT: X  321 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7679 (mtt90)
REVERT: Y   46 GLN cc_start: 0.8826 (tp40) cc_final: 0.8319 (tm-30)
REVERT: Y  117 LYS cc_start: 0.8239 (mttp) cc_final: 0.7696 (mptt)
REVERT: Y  161 TYR cc_start: 0.8211 (t80) cc_final: 0.6904 (t80)
REVERT: Y  254 TYR cc_start: 0.6264 (m-80) cc_final: 0.5016 (t80)
REVERT: Y  287 PHE cc_start: 0.7724 (m-80) cc_final: 0.6744 (m-80)
REVERT: Y  305 GLN cc_start: 0.8308 (mt0) cc_final: 0.8013 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2238
  time to fit residues: 39.3589
Evaluate side-chains
  86 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
X 191 HIS
Y  19 GLN
Y  46 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.179408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.138901 restraints weight = 8237.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.139549 restraints weight = 14314.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.140700 restraints weight = 9351.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5002  Z= 0.190
  Angle     :  0.599   7.707   6820  Z= 0.314
  Chirality :  0.044   0.221    790
  Planarity :  0.005   0.052    904
  Dihedral  :  3.816  17.331    725
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 10.45 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.99 (0.34), residues: 643
  helix:  2.15 (0.31), residues: 275
  sheet: -0.15 (0.47), residues: 115
  loop : -0.60 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 195 
 HIS   0.002   0.001   HIS X 170 
 PHE   0.027   0.003   PHE Y 252 
 TYR   0.020   0.002   TYR X 302 
 ARG   0.016   0.001   ARG Y 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  243)
  hydrogen bonds       : angle       4.36498 (  699)
  covalent geometry    : bond        0.00448 ( 5002)
  covalent geometry    : angle       0.59936 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7085 (tpt) cc_final: 0.6495 (tpp)
REVERT: X   12 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7982 (tt)
REVERT: X   37 ASP cc_start: 0.7606 (m-30) cc_final: 0.6935 (t0)
REVERT: X  120 LYS cc_start: 0.8417 (mttp) cc_final: 0.8183 (mttt)
REVERT: X  167 GLN cc_start: 0.7685 (pm20) cc_final: 0.7456 (pm20)
REVERT: X  241 ARG cc_start: 0.8243 (ptt90) cc_final: 0.7966 (ptm-80)
REVERT: X  295 LEU cc_start: 0.8610 (tt) cc_final: 0.8120 (tt)
REVERT: X  297 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8205 (ptm-80)
REVERT: Y   71 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7059 (tm-30)
REVERT: Y  161 TYR cc_start: 0.8403 (t80) cc_final: 0.7737 (t80)
REVERT: Y  220 PRO cc_start: 0.8017 (Cg_exo) cc_final: 0.7789 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6852 (m-80) cc_final: 0.5227 (t80)
REVERT: Y  302 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8215 (ptm160)
  outliers start: 27
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1991
  time to fit residues: 25.0688
Evaluate side-chains
  93 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  198 VAL
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain X residue  265 LEU
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   12 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  157 THR
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
X 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.176271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136767 restraints weight = 8220.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.132251 restraints weight = 12473.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.133485 restraints weight = 11865.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5002  Z= 0.225
  Angle     :  0.621   7.754   6820  Z= 0.327
  Chirality :  0.044   0.171    790
  Planarity :  0.006   0.058    904
  Dihedral  :  4.246  19.645    725
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 12.62 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.18 (0.32), residues: 643
  helix:  1.34 (0.31), residues: 276
  sheet: -0.47 (0.44), residues: 120
  loop : -0.92 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 195 
 HIS   0.002   0.001   HIS X 170 
 PHE   0.018   0.003   PHE Y 287 
 TYR   0.021   0.002   TYR Y  17 
 ARG   0.008   0.001   ARG X 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  243)
  hydrogen bonds       : angle       4.57870 (  699)
  covalent geometry    : bond        0.00535 ( 5002)
  covalent geometry    : angle       0.62056 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7348 (tpt) cc_final: 0.6898 (tpp)
REVERT: X   37 ASP cc_start: 0.8031 (m-30) cc_final: 0.7185 (t0)
REVERT: X  120 LYS cc_start: 0.8513 (mttp) cc_final: 0.8204 (mttt)
REVERT: X  167 GLN cc_start: 0.7744 (pm20) cc_final: 0.7525 (pm20)
REVERT: X  241 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8194 (ptm-80)
REVERT: Y   60 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8129 (pp)
REVERT: Y   71 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7042 (tm-30)
REVERT: Y  161 TYR cc_start: 0.8575 (t80) cc_final: 0.7807 (t80)
REVERT: Y  220 PRO cc_start: 0.8116 (Cg_exo) cc_final: 0.7888 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6887 (m-80) cc_final: 0.5134 (t80)
REVERT: Y  272 MET cc_start: 0.6821 (mmm) cc_final: 0.6604 (tpt)
REVERT: Y  283 PHE cc_start: 0.7544 (t80) cc_final: 0.7199 (t80)
REVERT: Y  302 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7978 (ptm-80)
  outliers start: 24
  outliers final: 16
  residues processed: 86
  average time/residue: 0.1921
  time to fit residues: 20.7098
Evaluate side-chains
  81 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   19 THR
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   60 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  157 THR
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  251 MET
Chi-restraints excluded: chain Y residue  302 ARG
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0030
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 42 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.3708

-------------------------------------------------------------------------------
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 = 0.4177 r_free = 0.4177 target = 0.179003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.138590 restraints weight = 8362.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.138903 restraints weight = 14351.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.139760 restraints weight = 10761.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5002  Z= 0.118
  Angle     :  0.557   8.202   6820  Z= 0.287
  Chirality :  0.042   0.176    790
  Planarity :  0.005   0.050    904
  Dihedral  :  4.054  18.685    725
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 14.00 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.41 (0.33), residues: 643
  helix:  1.59 (0.32), residues: 276
  sheet: -0.40 (0.45), residues: 121
  loop : -0.84 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP X 186 
 HIS   0.002   0.000   HIS X 325 
 PHE   0.014   0.002   PHE X  44 
 TYR   0.011   0.001   TYR Y  17 
 ARG   0.005   0.000   ARG X 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (  243)
  hydrogen bonds       : angle       4.32733 (  699)
  covalent geometry    : bond        0.00279 ( 5002)
  covalent geometry    : angle       0.55684 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.6959 (tpt) cc_final: 0.6401 (tpp)
REVERT: X   14 ILE cc_start: 0.8261 (mm) cc_final: 0.7923 (mm)
REVERT: X   37 ASP cc_start: 0.8001 (m-30) cc_final: 0.7268 (t0)
REVERT: X  120 LYS cc_start: 0.8456 (mttp) cc_final: 0.8193 (mttt)
REVERT: X  167 GLN cc_start: 0.7668 (pm20) cc_final: 0.7423 (pm20)
REVERT: Y  157 THR cc_start: 0.6693 (m) cc_final: 0.6293 (p)
REVERT: Y  161 TYR cc_start: 0.8418 (t80) cc_final: 0.7758 (t80)
REVERT: Y  197 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.7861 (p)
REVERT: Y  220 PRO cc_start: 0.8079 (Cg_exo) cc_final: 0.7873 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6784 (m-80) cc_final: 0.5124 (t80)
REVERT: Y  283 PHE cc_start: 0.7190 (t80) cc_final: 0.6970 (t80)
REVERT: Y  302 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8067 (ptm-80)
  outliers start: 21
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1871
  time to fit residues: 22.0260
Evaluate side-chains
  84 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  129 ASP
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  251 MET
Chi-restraints excluded: chain Y residue  302 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0270
   chunk 30 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
Y  19 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.179432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140372 restraints weight = 8054.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.133594 restraints weight = 8184.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.135416 restraints weight = 8912.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5002  Z= 0.130
  Angle     :  0.570   6.046   6820  Z= 0.294
  Chirality :  0.041   0.137    790
  Planarity :  0.005   0.050    904
  Dihedral  :  4.062  17.849    725
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 14.00 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.37 (0.33), residues: 643
  helix:  1.57 (0.32), residues: 276
  sheet: -0.32 (0.45), residues: 117
  loop : -0.95 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP X 186 
 HIS   0.002   0.000   HIS X 325 
 PHE   0.013   0.002   PHE X  44 
 TYR   0.010   0.001   TYR Y  17 
 ARG   0.004   0.000   ARG X 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03125 (  243)
  hydrogen bonds       : angle       4.32015 (  699)
  covalent geometry    : bond        0.00312 ( 5002)
  covalent geometry    : angle       0.56954 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7247 (tpt) cc_final: 0.6912 (tpp)
REVERT: X   37 ASP cc_start: 0.7658 (m-30) cc_final: 0.7073 (t0)
REVERT: X  120 LYS cc_start: 0.8410 (mttp) cc_final: 0.8145 (mttt)
REVERT: X  167 GLN cc_start: 0.7618 (pm20) cc_final: 0.7192 (pm20)
REVERT: Y  157 THR cc_start: 0.7038 (m) cc_final: 0.6576 (p)
REVERT: Y  161 TYR cc_start: 0.8560 (t80) cc_final: 0.7686 (t80)
REVERT: Y  197 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7961 (p)
REVERT: Y  220 PRO cc_start: 0.8084 (Cg_exo) cc_final: 0.7874 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6901 (m-80) cc_final: 0.5096 (t80)
REVERT: Y  283 PHE cc_start: 0.7822 (t80) cc_final: 0.7573 (t80)
REVERT: Y  302 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8002 (ptm-80)
  outliers start: 25
  outliers final: 18
  residues processed: 88
  average time/residue: 0.1948
  time to fit residues: 21.5734
Evaluate side-chains
  90 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  111 VAL
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  129 ASP
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   60 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 58 optimal weight:    0.0670
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5720

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.177804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138730 restraints weight = 8454.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.134731 restraints weight = 11031.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.136310 restraints weight = 10856.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5002  Z= 0.146
  Angle     :  0.576   6.447   6820  Z= 0.299
  Chirality :  0.042   0.262    790
  Planarity :  0.005   0.051    904
  Dihedral  :  4.202  20.405    725
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 15.58 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.24 (0.33), residues: 643
  helix:  1.50 (0.32), residues: 276
  sheet: -0.33 (0.45), residues: 115
  loop : -1.09 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP Y 279 
 HIS   0.001   0.000   HIS X 325 
 PHE   0.013   0.002   PHE X  44 
 TYR   0.011   0.001   TYR Y  17 
 ARG   0.005   0.000   ARG X 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03203 (  243)
  hydrogen bonds       : angle       4.39583 (  699)
  covalent geometry    : bond        0.00352 ( 5002)
  covalent geometry    : angle       0.57570 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7290 (tpt) cc_final: 0.6882 (tpp)
REVERT: X   37 ASP cc_start: 0.7888 (m-30) cc_final: 0.7235 (t0)
REVERT: X  120 LYS cc_start: 0.8429 (mttp) cc_final: 0.8153 (mttt)
REVERT: X  167 GLN cc_start: 0.7708 (pm20) cc_final: 0.7321 (pm20)
REVERT: X  168 PHE cc_start: 0.8599 (p90) cc_final: 0.8340 (p90)
REVERT: Y   60 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8109 (pp)
REVERT: Y   62 ASP cc_start: 0.7687 (t0) cc_final: 0.7466 (t0)
REVERT: Y  157 THR cc_start: 0.6813 (m) cc_final: 0.6372 (p)
REVERT: Y  161 TYR cc_start: 0.8475 (t80) cc_final: 0.7670 (t80)
REVERT: Y  197 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7888 (p)
REVERT: Y  220 PRO cc_start: 0.7959 (Cg_exo) cc_final: 0.7756 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6867 (m-80) cc_final: 0.5118 (t80)
REVERT: Y  287 PHE cc_start: 0.7074 (m-10) cc_final: 0.6553 (m-10)
REVERT: Y  302 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7946 (ptm-80)
  outliers start: 21
  outliers final: 15
  residues processed: 85
  average time/residue: 0.1863
  time to fit residues: 19.7951
Evaluate side-chains
  86 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  111 VAL
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  190 THR
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   60 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0770
   overall best weight:    0.8342

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

Flipped N/Q/H residues before XYZ refinement:
** Y  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.175881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.134581 restraints weight = 8351.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.130073 restraints weight = 9476.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.131729 restraints weight = 9901.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5002  Z= 0.186
  Angle     :  0.616  10.253   6820  Z= 0.320
  Chirality :  0.042   0.182    790
  Planarity :  0.005   0.050    904
  Dihedral  :  4.300  18.272    725
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 15.38 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.01 (0.33), residues: 643
  helix:  1.25 (0.32), residues: 275
  sheet: -0.39 (0.45), residues: 115
  loop : -1.16 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP Y 279 
 HIS   0.001   0.001   HIS X 191 
 PHE   0.018   0.002   PHE Y 283 
 TYR   0.015   0.001   TYR Y  17 
 ARG   0.005   0.001   ARG X 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  243)
  hydrogen bonds       : angle       4.62836 (  699)
  covalent geometry    : bond        0.00449 ( 5002)
  covalent geometry    : angle       0.61628 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7236 (tpt) cc_final: 0.6846 (tpp)
REVERT: X   37 ASP cc_start: 0.8065 (m-30) cc_final: 0.7327 (t0)
REVERT: X  120 LYS cc_start: 0.8423 (mttp) cc_final: 0.8108 (mttt)
REVERT: X  167 GLN cc_start: 0.7670 (pm20) cc_final: 0.7331 (pm20)
REVERT: X  168 PHE cc_start: 0.8648 (p90) cc_final: 0.8394 (p90)
REVERT: Y   60 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (pp)
REVERT: Y  157 THR cc_start: 0.7022 (m) cc_final: 0.6560 (p)
REVERT: Y  161 TYR cc_start: 0.8599 (t80) cc_final: 0.7729 (t80)
REVERT: Y  197 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8006 (p)
REVERT: Y  254 TYR cc_start: 0.6985 (m-80) cc_final: 0.5152 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 81
  average time/residue: 0.1869
  time to fit residues: 19.1409
Evaluate side-chains
  79 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  111 VAL
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  190 THR
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   12 LEU
Chi-restraints excluded: chain Y residue   60 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    0.1980
   chunk 40 optimal weight:    0.1980
   chunk 46 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0020
   chunk 60 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.2588

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

Flipped N/Q/H residues before XYZ refinement:
** Y  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.179034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.139721 restraints weight = 8432.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.137022 restraints weight = 12320.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138418 restraints weight = 11338.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5002  Z= 0.115
  Angle     :  0.563   6.918   6820  Z= 0.293
  Chirality :  0.041   0.143    790
  Planarity :  0.004   0.043    904
  Dihedral  :  4.142  16.381    725
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.16 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.28 (0.33), residues: 643
  helix:  1.55 (0.32), residues: 270
  sheet: -0.41 (0.44), residues: 110
  loop : -0.97 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.000   TRP Y 279 
 HIS   0.002   0.001   HIS X 325 
 PHE   0.014   0.002   PHE X  44 
 TYR   0.010   0.001   TYR Y  17 
 ARG   0.006   0.000   ARG X 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03075 (  243)
  hydrogen bonds       : angle       4.38260 (  699)
  covalent geometry    : bond        0.00273 ( 5002)
  covalent geometry    : angle       0.56331 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7004 (tpt) cc_final: 0.6407 (tpt)
REVERT: X   37 ASP cc_start: 0.8070 (m-30) cc_final: 0.7334 (t0)
REVERT: X  120 LYS cc_start: 0.8463 (mttp) cc_final: 0.8204 (mttt)
REVERT: X  167 GLN cc_start: 0.7604 (pm20) cc_final: 0.7324 (pm20)
REVERT: X  168 PHE cc_start: 0.8599 (p90) cc_final: 0.8386 (p90)
REVERT: Y   62 ASP cc_start: 0.7716 (t0) cc_final: 0.7454 (t0)
REVERT: Y  117 LYS cc_start: 0.8268 (mttp) cc_final: 0.7774 (mptt)
REVERT: Y  161 TYR cc_start: 0.8427 (t80) cc_final: 0.7613 (t80)
REVERT: Y  197 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7858 (p)
REVERT: Y  254 TYR cc_start: 0.6869 (m-80) cc_final: 0.5166 (t80)
REVERT: Y  283 PHE cc_start: 0.7877 (t80) cc_final: 0.7520 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 84
  average time/residue: 0.2068
  time to fit residues: 21.2900
Evaluate side-chains
  76 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  111 VAL
Chi-restraints excluded: chain X residue  129 ASP
Chi-restraints excluded: chain X residue  190 THR
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0670
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0010
   overall best weight:    0.3524

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

Flipped N/Q/H residues before XYZ refinement:
Y  19 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.178986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.143175 restraints weight = 8250.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.141608 restraints weight = 12065.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.142381 restraints weight = 11729.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5002  Z= 0.130
  Angle     :  0.619  15.167   6820  Z= 0.315
  Chirality :  0.042   0.145    790
  Planarity :  0.005   0.045    904
  Dihedral  :  4.130  15.677    725
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.34 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.14 (0.33), residues: 643
  helix:  1.34 (0.32), residues: 270
  sheet: -0.40 (0.44), residues: 110
  loop : -0.96 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP Y 279 
 HIS   0.002   0.001   HIS X 325 
 PHE   0.012   0.002   PHE X  44 
 TYR   0.009   0.001   TYR Y  17 
 ARG   0.010   0.000   ARG Y 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  243)
  hydrogen bonds       : angle       4.57531 (  699)
  covalent geometry    : bond        0.00313 ( 5002)
  covalent geometry    : angle       0.61880 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7321 (tpt) cc_final: 0.6641 (tpt)
REVERT: X   37 ASP cc_start: 0.8155 (m-30) cc_final: 0.7397 (t0)
REVERT: X  120 LYS cc_start: 0.8451 (mttp) cc_final: 0.8201 (mttt)
REVERT: X  167 GLN cc_start: 0.7632 (pm20) cc_final: 0.7227 (pm20)
REVERT: X  168 PHE cc_start: 0.8516 (p90) cc_final: 0.8303 (p90)
REVERT: Y   62 ASP cc_start: 0.7584 (t0) cc_final: 0.7346 (t0)
REVERT: Y  117 LYS cc_start: 0.8268 (mttp) cc_final: 0.7759 (mptt)
REVERT: Y  161 TYR cc_start: 0.8284 (t80) cc_final: 0.7584 (t80)
REVERT: Y  197 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7796 (p)
REVERT: Y  254 TYR cc_start: 0.6812 (m-80) cc_final: 0.5179 (t80)
REVERT: Y  283 PHE cc_start: 0.7674 (t80) cc_final: 0.7391 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1827
  time to fit residues: 16.8830
Evaluate side-chains
  74 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  190 THR
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0470
   chunk 28 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.177742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.136618 restraints weight = 8425.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132409 restraints weight = 10353.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133829 restraints weight = 10047.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.4329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5002  Z= 0.158
  Angle     :  0.649  12.700   6820  Z= 0.328
  Chirality :  0.043   0.157    790
  Planarity :  0.005   0.045    904
  Dihedral  :  4.217  16.823    725
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.95 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.15 (0.33), residues: 643
  helix:  0.98 (0.32), residues: 276
  sheet: -0.40 (0.45), residues: 115
  loop : -1.11 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y 279 
 HIS   0.002   0.001   HIS X 325 
 PHE   0.013   0.002   PHE X  44 
 TYR   0.007   0.001   TYR X  22 
 ARG   0.009   0.000   ARG Y 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  243)
  hydrogen bonds       : angle       4.71478 (  699)
  covalent geometry    : bond        0.00383 ( 5002)
  covalent geometry    : angle       0.64905 ( 6820)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7270 (tpt) cc_final: 0.6901 (tpp)
REVERT: X   37 ASP cc_start: 0.8179 (m-30) cc_final: 0.7361 (t0)
REVERT: X  120 LYS cc_start: 0.8405 (mttp) cc_final: 0.8079 (mttt)
REVERT: X  167 GLN cc_start: 0.7620 (pm20) cc_final: 0.7241 (pm20)
REVERT: X  168 PHE cc_start: 0.8653 (p90) cc_final: 0.8417 (p90)
REVERT: X  251 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6766 (tm-30)
REVERT: Y   62 ASP cc_start: 0.7585 (t0) cc_final: 0.7364 (t0)
REVERT: Y  117 LYS cc_start: 0.8325 (mttp) cc_final: 0.7802 (mptt)
REVERT: Y  147 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7401 (mtm-85)
REVERT: Y  161 TYR cc_start: 0.8564 (t80) cc_final: 0.7584 (t80)
REVERT: Y  197 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.7986 (p)
REVERT: Y  254 TYR cc_start: 0.6903 (m-80) cc_final: 0.5102 (t80)
REVERT: Y  283 PHE cc_start: 0.7953 (t80) cc_final: 0.7615 (t80)
  outliers start: 12
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1923
  time to fit residues: 18.6305
Evaluate side-chains
  75 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  129 ASP
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    0.0050
   chunk 1 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 46 optimal weight:    0.3980
   chunk 33 optimal weight:    0.0970
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.2792

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.179399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.138629 restraints weight = 8413.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.135026 restraints weight = 13455.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.137103 restraints weight = 10665.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5002  Z= 0.120
  Angle     :  0.623  12.706   6820  Z= 0.313
  Chirality :  0.042   0.167    790
  Planarity :  0.004   0.044    904
  Dihedral  :  4.126  15.538    725
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.95 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.04 (0.33), residues: 643
  helix:  1.21 (0.32), residues: 270
  sheet: -0.46 (0.44), residues: 110
  loop : -0.95 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y 250 
 HIS   0.002   0.001   HIS X 325 
 PHE   0.012   0.001   PHE X  44 
 TYR   0.005   0.001   TYR X 178 
 ARG   0.010   0.000   ARG Y 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  243)
  hydrogen bonds       : angle       4.57964 (  699)
  covalent geometry    : bond        0.00285 ( 5002)
  covalent geometry    : angle       0.62280 ( 6820)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1899.87 seconds
wall clock time: 33 minutes 48.79 seconds (2028.79 seconds total)