Starting phenix.real_space_refine
on Thu Mar  6 05:01:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnd_50590/03_2025/9fnd_50590.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnd_50590/03_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_50590/03_2025/9fnd_50590.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnd_50590/03_2025/9fnd_50590.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnd_50590/03_2025/9fnd_50590.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnd_50590/03_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-5624/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: 3.43, per 1000 atoms: 0.70
  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: 1.16
  Conformation dependent library (CDL) restraints added in 613.2 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: 0.52
  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: 1.17

  Time building geometry restraints manager: 1.39 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:             0.690
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.300
  Find NCS groups from input model:        0.060
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.090
-------------------------------------------------------------------------------
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= 0.116
  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 

*********************** 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  : 0.543 
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: 0.2268
  time to fit residues: 39.7585
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  : 0.542 
-------------------------------------------------------------------------------
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 = 0.139548 restraints weight = 14316.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.140704 restraints weight = 9350.790|
|-----------------------------------------------------------------------------|
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= 0.295
  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 

*********************** 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  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7084 (tpt) cc_final: 0.6494 (tpp)
REVERT: X   12 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7983 (tt)
REVERT: X   37 ASP cc_start: 0.7605 (m-30) cc_final: 0.6933 (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: 0.7967 (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: 0.7317 (tm-30) cc_final: 0.7060 (tm-30)
REVERT: Y  161 TYR cc_start: 0.8403 (t80) cc_final: 0.7738 (t80)
REVERT: Y  220 PRO cc_start: 0.8017 (Cg_exo) cc_final: 0.7789 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6853 (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: 0.2010
  time to fit residues: 25.4566
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  : 0.480 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0570
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.179544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139269 restraints weight = 8178.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.135979 restraints weight = 11804.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137508 restraints weight = 11432.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3208

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= 0.239
  Angle     :  0.558   5.295   6820  Z= 0.293
  Chirality :  0.042   0.159    790
  Planarity :  0.005   0.053    904
  Dihedral  :  3.969  18.135    725
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 13.81 %
    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:  0.55 (0.33), residues: 643
  helix:  1.69 (0.31), residues: 277
  sheet: -0.25 (0.46), residues: 114
  loop : -0.81 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Y 250 
 HIS   0.001   0.001   HIS X 325 
 PHE   0.017   0.002   PHE Y 287 
 TYR   0.018   0.002   TYR X 178 
 ARG   0.008   0.000   ARG X 171 

*********************** 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
  99 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7331 (tpt) cc_final: 0.6851 (tpp)
REVERT: X   12 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7457 (tt)
REVERT: X   37 ASP cc_start: 0.7781 (m-30) cc_final: 0.7112 (t0)
REVERT: X  120 LYS cc_start: 0.8462 (mttp) cc_final: 0.8187 (mttt)
REVERT: X  167 GLN cc_start: 0.7736 (pm20) cc_final: 0.7532 (pm20)
REVERT: Y   59 ASP cc_start: 0.7872 (t70) cc_final: 0.7655 (t70)
REVERT: Y  161 TYR cc_start: 0.8437 (t80) cc_final: 0.7585 (t80)
REVERT: Y  197 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7889 (p)
REVERT: Y  220 PRO cc_start: 0.8081 (Cg_exo) cc_final: 0.7839 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6819 (m-80) cc_final: 0.5122 (t80)
REVERT: Y  302 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7940 (ptm-80)
  outliers start: 22
  outliers final: 15
  residues processed: 89
  average time/residue: 0.2277
  time to fit residues: 25.5813
Evaluate side-chains
  83 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
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  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   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:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    0.2980
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.180245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.139109 restraints weight = 8392.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.135406 restraints weight = 10912.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.136931 restraints weight = 10403.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5002  Z= 0.190
  Angle     :  0.553  10.177   6820  Z= 0.284
  Chirality :  0.041   0.161    790
  Planarity :  0.005   0.051    904
  Dihedral  :  3.964  18.179    725
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.21 %
    Favored  : 82.84 %
  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:  0.46 (0.33), residues: 643
  helix:  1.57 (0.32), residues: 277
  sheet: -0.26 (0.45), residues: 119
  loop : -0.81 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP X 195 
 HIS   0.001   0.000   HIS X 325 
 PHE   0.012   0.002   PHE X  44 
 TYR   0.012   0.001   TYR Y  17 
 ARG   0.005   0.000   ARG X 171 

*********************** 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
  93 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7172 (tpt) cc_final: 0.6437 (tpt)
REVERT: X   12 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8139 (tt)
REVERT: X   37 ASP cc_start: 0.7833 (m-30) cc_final: 0.7144 (t0)
REVERT: X  120 LYS cc_start: 0.8423 (mttp) cc_final: 0.8153 (mttt)
REVERT: X  167 GLN cc_start: 0.7695 (pm20) cc_final: 0.7442 (pm20)
REVERT: Y   59 ASP cc_start: 0.7878 (t70) cc_final: 0.7579 (t70)
REVERT: Y   71 GLU cc_start: 0.7241 (tm-30) cc_final: 0.7001 (tm-30)
REVERT: Y  157 THR cc_start: 0.6768 (m) cc_final: 0.6459 (p)
REVERT: Y  161 TYR cc_start: 0.8433 (t80) cc_final: 0.7538 (t80)
REVERT: Y  197 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7848 (p)
REVERT: Y  220 PRO cc_start: 0.8063 (Cg_exo) cc_final: 0.7836 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6792 (m-80) cc_final: 0.5053 (t80)
REVERT: Y  302 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8205 (ptm-80)
  outliers start: 20
  outliers final: 13
  residues processed: 85
  average time/residue: 0.2032
  time to fit residues: 21.5899
Evaluate side-chains
  83 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 38 optimal weight:    0.1980
   chunk 30 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4147 r_free = 0.4147 target = 0.176319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135824 restraints weight = 8315.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132117 restraints weight = 12828.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.134203 restraints weight = 11764.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5002  Z= 0.318
  Angle     :  0.607   7.316   6820  Z= 0.314
  Chirality :  0.042   0.137    790
  Planarity :  0.005   0.051    904
  Dihedral  :  4.232  18.399    725
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 14.40 %
    Favored  : 80.67 %
  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:  0.06 (0.33), residues: 643
  helix:  1.22 (0.31), residues: 277
  sheet: -0.41 (0.45), residues: 121
  loop : -1.04 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP X 186 
 HIS   0.001   0.001   HIS Y  80 
 PHE   0.018   0.003   PHE Y 287 
 TYR   0.011   0.001   TYR X  22 
 ARG   0.004   0.000   ARG X 171 

*********************** 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
  94 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7485 (tpt) cc_final: 0.7122 (tpp)
REVERT: X   37 ASP cc_start: 0.8074 (m-30) cc_final: 0.7298 (t0)
REVERT: X  120 LYS cc_start: 0.8511 (mttp) cc_final: 0.8144 (mttt)
REVERT: X  167 GLN cc_start: 0.7689 (pm20) cc_final: 0.7412 (pm20)
REVERT: X  168 PHE cc_start: 0.8602 (p90) cc_final: 0.8313 (p90)
REVERT: Y   60 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8005 (pp)
REVERT: Y   78 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7669 (m)
REVERT: Y   92 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (tp)
REVERT: Y  157 THR cc_start: 0.6817 (m) cc_final: 0.6508 (p)
REVERT: Y  161 TYR cc_start: 0.8554 (t80) cc_final: 0.7851 (t80)
REVERT: Y  197 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.7973 (p)
REVERT: Y  254 TYR cc_start: 0.6814 (m-80) cc_final: 0.5124 (t80)
REVERT: Y  302 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7917 (ptm-80)
  outliers start: 25
  outliers final: 16
  residues processed: 86
  average time/residue: 0.2006
  time to fit residues: 21.5229
Evaluate side-chains
  87 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
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   12 LEU
Chi-restraints excluded: chain Y residue   60 LEU
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   92 ILE
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:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 4 optimal weight:    0.1980
   chunk 5 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.177224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138205 restraints weight = 8390.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.134784 restraints weight = 12835.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.135857 restraints weight = 12284.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5002  Z= 0.227
  Angle     :  0.586   6.749   6820  Z= 0.304
  Chirality :  0.041   0.139    790
  Planarity :  0.005   0.048    904
  Dihedral  :  4.262  17.818    725
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 14.40 %
    Favored  : 81.26 %
  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:  0.09 (0.33), residues: 643
  helix:  1.29 (0.32), residues: 275
  sheet: -0.39 (0.45), residues: 117
  loop : -1.05 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Y 279 
 HIS   0.001   0.000   HIS X 325 
 PHE   0.015   0.002   PHE X  44 
 TYR   0.008   0.001   TYR X 178 
 ARG   0.004   0.000   ARG X 171 

*********************** 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
  90 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7069 (tpt) cc_final: 0.6733 (tpp)
REVERT: X   37 ASP cc_start: 0.8089 (m-30) cc_final: 0.7330 (t0)
REVERT: X  120 LYS cc_start: 0.8448 (mttp) cc_final: 0.8184 (mttt)
REVERT: Y   60 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8085 (pp)
REVERT: Y  161 TYR cc_start: 0.8454 (t80) cc_final: 0.7727 (t80)
REVERT: Y  197 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.7913 (p)
REVERT: Y  254 TYR cc_start: 0.6738 (m-80) cc_final: 0.5072 (t80)
REVERT: Y  302 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7997 (ptm-80)
  outliers start: 22
  outliers final: 15
  residues processed: 83
  average time/residue: 0.2039
  time to fit residues: 21.6960
Evaluate side-chains
  82 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
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
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0770
   chunk 57 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0670
   chunk 0 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4159 r_free = 0.4159 target = 0.177590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.138814 restraints weight = 8299.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.135089 restraints weight = 10737.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.136156 restraints weight = 12173.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5002  Z= 0.209
  Angle     :  0.583   7.046   6820  Z= 0.301
  Chirality :  0.041   0.131    790
  Planarity :  0.004   0.046    904
  Dihedral  :  4.206  16.909    725
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.78 %
    Favored  : 79.88 %
  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:  1.33 (0.32), residues: 275
  sheet: -0.35 (0.45), residues: 115
  loop : -1.04 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Y 250 
 HIS   0.001   0.001   HIS X 325 
 PHE   0.014   0.002   PHE X  44 
 TYR   0.007   0.001   TYR X 178 
 ARG   0.005   0.000   ARG X 237 

*********************** 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
  91 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7361 (tpt) cc_final: 0.6835 (tpt)
REVERT: X   37 ASP cc_start: 0.8089 (m-30) cc_final: 0.7277 (t0)
REVERT: X  120 LYS cc_start: 0.8502 (mttp) cc_final: 0.8251 (mttt)
REVERT: X  167 GLN cc_start: 0.7580 (pm20) cc_final: 0.7282 (pm20)
REVERT: Y   78 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7616 (m)
REVERT: Y  117 LYS cc_start: 0.8364 (mttp) cc_final: 0.7957 (mptt)
REVERT: Y  161 TYR cc_start: 0.8486 (t80) cc_final: 0.7676 (t80)
REVERT: Y  197 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7890 (p)
REVERT: Y  254 TYR cc_start: 0.6781 (m-80) cc_final: 0.5096 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 84
  average time/residue: 0.2536
  time to fit residues: 26.8306
Evaluate side-chains
  80 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
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  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   78 VAL
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6558

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.176330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135786 restraints weight = 8450.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.134477 restraints weight = 16070.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.136853 restraints weight = 12133.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5002  Z= 0.250
  Angle     :  0.599   7.200   6820  Z= 0.309
  Chirality :  0.042   0.197    790
  Planarity :  0.005   0.044    904
  Dihedral  :  4.233  17.320    725
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.98 %
    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:  0.01 (0.33), residues: 643
  helix:  1.24 (0.32), residues: 275
  sheet: -0.43 (0.45), residues: 115
  loop : -1.12 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP X 186 
 HIS   0.002   0.001   HIS X 191 
 PHE   0.014   0.002   PHE X  44 
 TYR   0.007   0.001   TYR X  22 
 ARG   0.006   0.000   ARG Y 302 

*********************** 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: 22
    poor density    : 66
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7169 (tpt) cc_final: 0.6741 (tpp)
REVERT: X   37 ASP cc_start: 0.8016 (m-30) cc_final: 0.7284 (t0)
REVERT: X  120 LYS cc_start: 0.8452 (mttp) cc_final: 0.8082 (mttt)
REVERT: X  168 PHE cc_start: 0.8618 (p90) cc_final: 0.8356 (p90)
REVERT: Y   60 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7934 (pp)
REVERT: Y   78 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7744 (m)
REVERT: Y  117 LYS cc_start: 0.8312 (mttp) cc_final: 0.7992 (mptt)
REVERT: Y  161 TYR cc_start: 0.8468 (t80) cc_final: 0.7674 (t80)
REVERT: Y  197 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7901 (p)
REVERT: Y  254 TYR cc_start: 0.6775 (m-80) cc_final: 0.5135 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1996
  time to fit residues: 20.3129
Evaluate side-chains
  81 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
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  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   78 VAL
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 1 optimal weight:    0.1980
   chunk 42 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0030
   chunk 40 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.3990

-------------------------------------------------------------------------------
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 = 0.4161 r_free = 0.4161 target = 0.177843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.137463 restraints weight = 8337.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.135534 restraints weight = 16107.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.137773 restraints weight = 12547.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5002  Z= 0.196
  Angle     :  0.610  14.381   6820  Z= 0.305
  Chirality :  0.041   0.163    790
  Planarity :  0.004   0.044    904
  Dihedral  :  4.172  15.913    725
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.57 %
    Favored  : 79.88 %
  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: -0.00 (0.33), residues: 643
  helix:  1.19 (0.32), residues: 274
  sheet: -0.52 (0.45), residues: 110
  loop : -1.00 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP Y 250 
 HIS   0.002   0.001   HIS X 191 
 PHE   0.013   0.002   PHE X  44 
 TYR   0.006   0.001   TYR Y  17 
 ARG   0.004   0.000   ARG X 280 

*********************** 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
  85 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7381 (tpt) cc_final: 0.7029 (tpt)
REVERT: X   37 ASP cc_start: 0.8028 (m-30) cc_final: 0.7296 (t0)
REVERT: X  120 LYS cc_start: 0.8472 (mttp) cc_final: 0.8221 (mttt)
REVERT: X  168 PHE cc_start: 0.8615 (p90) cc_final: 0.8329 (p90)
REVERT: Y   78 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.6841 (p)
REVERT: Y  117 LYS cc_start: 0.8264 (mttp) cc_final: 0.7940 (mptt)
REVERT: Y  160 TYR cc_start: 0.6886 (t80) cc_final: 0.6654 (t80)
REVERT: Y  161 TYR cc_start: 0.8417 (t80) cc_final: 0.7340 (t80)
REVERT: Y  197 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7897 (p)
  outliers start: 18
  outliers final: 13
  residues processed: 80
  average time/residue: 0.2652
  time to fit residues: 27.4204
Evaluate side-chains
  74 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  118 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   60 LEU
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    0.0570
   chunk 55 optimal weight:    7.9990
   chunk 61 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.4158 r_free = 0.4158 target = 0.177436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137774 restraints weight = 8436.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132341 restraints weight = 11079.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133791 restraints weight = 10494.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5002  Z= 0.230
  Angle     :  0.635  12.568   6820  Z= 0.324
  Chirality :  0.042   0.148    790
  Planarity :  0.004   0.044    904
  Dihedral  :  4.173  16.484    725
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  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: -0.15 (0.33), residues: 643
  helix:  1.00 (0.32), residues: 275
  sheet: -0.48 (0.45), residues: 115
  loop : -1.07 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 292 
 HIS   0.002   0.001   HIS X 191 
 PHE   0.013   0.002   PHE X  44 
 TYR   0.006   0.001   TYR Y  17 
 ARG   0.005   0.000   ARG Y 147 

********************** 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
  80 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7142 (tpt) cc_final: 0.6785 (tpp)
REVERT: X   37 ASP cc_start: 0.8087 (m-30) cc_final: 0.7243 (t0)
REVERT: X   90 LEU cc_start: 0.8257 (mp) cc_final: 0.8046 (mt)
REVERT: X  120 LYS cc_start: 0.8448 (mttp) cc_final: 0.8057 (mttt)
REVERT: X  167 GLN cc_start: 0.7638 (pm20) cc_final: 0.7264 (pm20)
REVERT: X  168 PHE cc_start: 0.8658 (p90) cc_final: 0.8384 (p90)
REVERT: X  251 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6740 (tm-30)
REVERT: X  252 ARG cc_start: 0.6961 (mmp80) cc_final: 0.6503 (mmp80)
REVERT: Y   60 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7952 (pp)
REVERT: Y   78 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.6645 (p)
REVERT: Y  117 LYS cc_start: 0.8269 (mttp) cc_final: 0.7743 (mptt)
REVERT: Y  160 TYR cc_start: 0.7002 (t80) cc_final: 0.6674 (t80)
REVERT: Y  161 TYR cc_start: 0.8538 (t80) cc_final: 0.7375 (t80)
REVERT: Y  197 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7970 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 75
  average time/residue: 0.2160
  time to fit residues: 20.4426
Evaluate side-chains
  75 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
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   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 56 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0570
   chunk 33 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.2898

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.179182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.140277 restraints weight = 8417.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.140419 restraints weight = 14948.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.141652 restraints weight = 11692.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5002  Z= 0.183
  Angle     :  0.616  12.657   6820  Z= 0.313
  Chirality :  0.041   0.195    790
  Planarity :  0.004   0.044    904
  Dihedral  :  4.063  15.787    725
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.75 %
    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:  0.05 (0.33), residues: 643
  helix:  1.21 (0.32), residues: 269
  sheet: -0.47 (0.45), residues: 110
  loop : -0.92 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP Y 250 
 HIS   0.002   0.001   HIS X 325 
 PHE   0.012   0.001   PHE X  44 
 TYR   0.006   0.001   TYR Y  17 
 ARG   0.004   0.000   ARG X 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2055.49 seconds
wall clock time: 37 minutes 28.94 seconds (2248.94 seconds total)