Starting phenix.real_space_refine
on Sat Apr 26 17:19:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n3b_9350/04_2025/6n3b_9350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n3b_9350/04_2025/6n3b_9350.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6n3b_9350/04_2025/6n3b_9350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n3b_9350/04_2025/6n3b_9350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n3b_9350/04_2025/6n3b_9350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n3b_9350/04_2025/6n3b_9350.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   1.000
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      55      5.16       5
     C    1680      2.51       5
     N     480      2.21       5
     O     520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2735
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 260
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
    Chain: "B"
      Number of atoms: 287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 287
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 2, 'TRANS': 38}
  Restraints were copied for chains:
    C, E, G, I, D, F, H, J
  Time building chain proxies: 1.26, per 1000 atoms: 0.46
  Number of scatterers: 2735
  At special positions: 0
  Unit cell: (67.032, 82.992, 48.944, 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      55     16.00
     O     520      8.00
     N     480      7.00
     C    1680      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 324.6 milliseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  690

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 314 through 318
      removed outlier: 6.630A  pdb=" N   GLY C 314 " --> pdb=" O   ALA E 315 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   SER E 317 " --> pdb=" O   GLY C 314 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE C 316 " --> pdb=" O   SER E 317 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY E 314 " --> pdb=" O   ALA G 315 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   SER G 317 " --> pdb=" O   GLY E 314 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   PHE E 316 " --> pdb=" O   SER G 317 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY A 314 " --> pdb=" O   ALA I 315 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   SER I 317 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE A 316 " --> pdb=" O   SER I 317 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 321 through 322
      removed outlier: 7.187A  pdb=" N   ALA A 321 " --> pdb=" O   MET G 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 334
      removed outlier: 5.591A  pdb=" N   ALA A 329 " --> pdb=" O   LEU G 330 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   SER G 332 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   GLN A 331 " --> pdb=" O   SER G 332 " (cutoff:3.500A)
      removed outlier: 8.531A  pdb=" N   TRP G 334 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER A 333 " --> pdb=" O   TRP G 334 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 315 through 318
      removed outlier: 6.407A  pdb=" N   ALA B 315 " --> pdb=" O   PHE H 316 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ILE H 318 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   SER B 317 " --> pdb=" O   ILE H 318 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 321 through 323
      removed outlier: 5.796A  pdb=" N   ALA B 321 " --> pdb=" O   MET H 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.070A  pdb=" N   ALA D 328 " --> pdb=" O   ALA F 329 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ALA F 328 " --> pdb=" O   ALA H 329 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU H 330 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ALA B 328 " --> pdb=" O   ALA J 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 337 through 343
      removed outlier: 6.119A  pdb=" N   MET D 337 " --> pdb=" O   GLY F 338 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   LEU F 340 " --> pdb=" O   MET D 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   MET D 339 " --> pdb=" O   LEU F 340 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   SER F 342 " --> pdb=" O   MET D 339 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA D 341 " --> pdb=" O   SER F 342 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   MET F 337 " --> pdb=" O   GLY H 338 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   LEU H 340 " --> pdb=" O   MET F 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   MET F 339 " --> pdb=" O   LEU H 340 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   SER H 342 " --> pdb=" O   MET F 339 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ALA F 341 " --> pdb=" O   SER H 342 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   MET B 337 " --> pdb=" O   GLY J 338 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   LEU J 340 " --> pdb=" O   MET B 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   MET B 339 " --> pdb=" O   LEU J 340 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   SER J 342 " --> pdb=" O   MET B 339 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA B 341 " --> pdb=" O   SER J 342 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 346 through 347
      removed outlier: 3.514A  pdb=" N   SER D 347 " --> pdb=" O   GLN F 346 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER F 347 " --> pdb=" O   GLN H 346 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   GLN B 346 " --> pdb=" O   SER H 347 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER B 347 " --> pdb=" O   GLN J 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    44 hydrogen bonds defined for protein.
    132 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.60

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 813
        1.33 -     1.45: 450
        1.45 -     1.57: 1407
        1.57 -     1.69: 0
        1.69 -     1.80: 110
  Bond restraints: 2780
  Sorted by residual:
  bond pdb=" CB  TRP B 334 "
       pdb=" CG  TRP B 334 "
    ideal  model  delta    sigma   weight residual
    1.498  1.435  0.063 3.10e-02 1.04e+03 4.18e+00
  bond pdb=" CB  TRP J 334 "
       pdb=" CG  TRP J 334 "
    ideal  model  delta    sigma   weight residual
    1.498  1.435  0.063 3.10e-02 1.04e+03 4.15e+00
  bond pdb=" CB  TRP D 334 "
       pdb=" CG  TRP D 334 "
    ideal  model  delta    sigma   weight residual
    1.498  1.435  0.063 3.10e-02 1.04e+03 4.13e+00
  bond pdb=" CB  TRP H 334 "
       pdb=" CG  TRP H 334 "
    ideal  model  delta    sigma   weight residual
    1.498  1.435  0.063 3.10e-02 1.04e+03 4.12e+00
  bond pdb=" CB  TRP F 334 "
       pdb=" CG  TRP F 334 "
    ideal  model  delta    sigma   weight residual
    1.498  1.435  0.063 3.10e-02 1.04e+03 4.12e+00
  ... (remaining 2775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 3237
        1.61 -     3.22: 375
        3.22 -     4.83: 88
        4.83 -     6.44: 15
        6.44 -     8.05: 10
  Bond angle restraints: 3725
  Sorted by residual:
  angle pdb=" CA  ASN B 345 "
        pdb=" CB  ASN B 345 "
        pdb=" CG  ASN B 345 "
      ideal   model   delta    sigma   weight residual
     112.60  115.81   -3.21 1.00e+00 1.00e+00 1.03e+01
  angle pdb=" CA  ASN F 345 "
        pdb=" CB  ASN F 345 "
        pdb=" CG  ASN F 345 "
      ideal   model   delta    sigma   weight residual
     112.60  115.79   -3.19 1.00e+00 1.00e+00 1.02e+01
  angle pdb=" CA  ASN D 345 "
        pdb=" CB  ASN D 345 "
        pdb=" CG  ASN D 345 "
      ideal   model   delta    sigma   weight residual
     112.60  115.78   -3.18 1.00e+00 1.00e+00 1.01e+01
  angle pdb=" CA  ASN H 345 "
        pdb=" CB  ASN H 345 "
        pdb=" CG  ASN H 345 "
      ideal   model   delta    sigma   weight residual
     112.60  115.77   -3.17 1.00e+00 1.00e+00 1.00e+01
  angle pdb=" CA  ASN J 345 "
        pdb=" CB  ASN J 345 "
        pdb=" CG  ASN J 345 "
      ideal   model   delta    sigma   weight residual
     112.60  115.76   -3.16 1.00e+00 1.00e+00 1.00e+01
  ... (remaining 3720 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.12: 1520
       14.12 -    28.25: 125
       28.25 -    42.37: 15
       42.37 -    56.49: 0
       56.49 -    70.61: 5
  Dihedral angle restraints: 1665
    sinusoidal: 600
      harmonic: 1065
  Sorted by residual:
  dihedral pdb=" CA  MET H 336 "
           pdb=" C   MET H 336 "
           pdb=" N   MET H 337 "
           pdb=" CA  MET H 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.36  -25.64     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  MET J 336 "
           pdb=" C   MET J 336 "
           pdb=" N   MET J 337 "
           pdb=" CA  MET J 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.36  -25.64     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  MET B 336 "
           pdb=" C   MET B 336 "
           pdb=" N   MET B 337 "
           pdb=" CA  MET B 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.41  -25.59     0      5.00e+00 4.00e-02 2.62e+01
  ... (remaining 1662 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 169
       0.029 -    0.057: 108
       0.057 -    0.086: 38
       0.086 -    0.115: 55
       0.115 -    0.143: 5
  Chirality restraints: 375
  Sorted by residual:
  chirality pdb=" CA  ILE D 318 "
            pdb=" N   ILE D 318 "
            pdb=" C   ILE D 318 "
            pdb=" CB  ILE D 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  ILE J 318 "
            pdb=" N   ILE J 318 "
            pdb=" C   ILE J 318 "
            pdb=" CB  ILE J 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  ILE H 318 "
            pdb=" N   ILE H 318 "
            pdb=" C   ILE H 318 "
            pdb=" CB  ILE H 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 372 not shown)

  Planarity restraints: 505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H 348 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO H 349 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO H 349 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H 349 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY J 348 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO J 349 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO J 349 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO J 349 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 348 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.22e+00
        pdb=" N   PRO B 349 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 349 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 349 "    0.028 5.00e-02 4.00e+02
  ... (remaining 502 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 626
        2.78 -     3.31: 2424
        3.31 -     3.84: 4457
        3.84 -     4.37: 5236
        4.37 -     4.90: 9699
  Nonbonded interactions: 22442
  Sorted by model distance:
  nonbonded pdb=" O   MET C 311 "
            pdb=" N   MET E 311 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" N   MET A 311 "
            pdb=" O   MET G 311 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   MET E 311 "
            pdb=" N   MET G 311 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   MET A 311 "
            pdb=" N   MET I 311 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   GLN B 344 "
            pdb=" NE2 GLN G 331 "
     model   vdw
     2.360 3.120
  ... (remaining 22437 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
}

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:             0.130
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.510
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
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      :  0.010   0.063   2780  Z= 0.409
  Angle     :  1.207   8.052   3725  Z= 0.650
  Chirality :  0.054   0.143    375
  Planarity :  0.009   0.051    505
  Dihedral  : 11.404  70.614    975
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 20.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.70 %
    Favored  : 86.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.17 (0.24), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.18), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP D 334 
 PHE   0.035   0.009   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29686 (   44)
  hydrogen bonds       : angle      14.00127 (  132)
  covalent geometry    : bond        0.00960 ( 2780)
  covalent geometry    : angle       1.20695 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B  313 PHE cc_start: 0.6918 (m-10) cc_final: 0.6592 (m-80)
REVERT: B  334 TRP cc_start: 0.8783 (p-90) cc_final: 0.7830 (p-90)
REVERT: B  342 SER cc_start: 0.8351 (m) cc_final: 0.8000 (p)
REVERT: D  316 PHE cc_start: 0.7542 (p90) cc_final: 0.5855 (m-80)
REVERT: D  334 TRP cc_start: 0.8162 (p-90) cc_final: 0.4016 (t60)
REVERT: D  337 MET cc_start: 0.7292 (ptp) cc_final: 0.5921 (mmp)
REVERT: D  344 GLN cc_start: 0.7142 (pt0) cc_final: 0.6919 (tt0)
REVERT: E  336 MET cc_start: 0.7385 (mtt) cc_final: 0.7118 (mtt)
REVERT: F  323 MET cc_start: 0.6223 (ttp) cc_final: 0.5182 (mtt)
REVERT: F  334 TRP cc_start: 0.8681 (p-90) cc_final: 0.8042 (p-90)
REVERT: G  323 MET cc_start: 0.7210 (ptm) cc_final: 0.6992 (ptm)
REVERT: H  334 TRP cc_start: 0.8604 (p-90) cc_final: 0.8011 (p-90)
REVERT: H  342 SER cc_start: 0.8294 (m) cc_final: 0.7925 (p)
REVERT: I  323 MET cc_start: 0.7277 (ptm) cc_final: 0.6947 (ptm)
REVERT: J  313 PHE cc_start: 0.6858 (m-10) cc_final: 0.6530 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1107
  time to fit residues: 16.4333
Evaluate side-chains
  82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:   20.0000
   chunk 10 optimal weight:   30.0000
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 31 optimal weight:    0.4980
   chunk 21 optimal weight:    9.9990
   overall best weight:    5.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 346 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 346 GLN
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 346 GLN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 343 GLN
I 344 GLN
I 346 GLN
J 344 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.170991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.125598 restraints weight = 5898.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.129108 restraints weight = 3050.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.131141 restraints weight = 2027.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2780  Z= 0.182
  Angle     :  0.849  15.817   3725  Z= 0.432
  Chirality :  0.045   0.157    375
  Planarity :  0.007   0.054    505
  Dihedral  :  7.092  23.140    375
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 24.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.36 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.29 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.03 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP J 334 
 PHE   0.036   0.003   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05235 (   44)
  hydrogen bonds       : angle      10.69330 (  132)
  covalent geometry    : bond        0.00407 ( 2780)
  covalent geometry    : angle       0.84917 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: D  316 PHE cc_start: 0.7606 (p90) cc_final: 0.6079 (m-80)
REVERT: D  319 ASN cc_start: 0.8462 (p0) cc_final: 0.8176 (p0)
REVERT: D  334 TRP cc_start: 0.8187 (p-90) cc_final: 0.3619 (m100)
REVERT: D  337 MET cc_start: 0.7289 (ptp) cc_final: 0.5877 (mmp)
REVERT: D  344 GLN cc_start: 0.7456 (pt0) cc_final: 0.7201 (tt0)
REVERT: F  323 MET cc_start: 0.6802 (ttp) cc_final: 0.5273 (mtt)
REVERT: F  334 TRP cc_start: 0.8495 (p-90) cc_final: 0.7802 (p-90)
REVERT: G  323 MET cc_start: 0.7535 (ptm) cc_final: 0.7120 (ptp)
REVERT: I  323 MET cc_start: 0.7374 (ptm) cc_final: 0.6800 (ptm)
REVERT: I  339 MET cc_start: 0.7470 (mpt) cc_final: 0.7176 (mpt)
REVERT: J  313 PHE cc_start: 0.6099 (m-10) cc_final: 0.5214 (p90)
REVERT: J  323 MET cc_start: 0.5209 (ttt) cc_final: 0.4220 (mtp)
  outliers start: 7
  outliers final: 4
  residues processed: 103
  average time/residue: 0.1098
  time to fit residues: 14.2449
Evaluate side-chains
  88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain E residue  344 GLN
Chi-restraints excluded: chain H residue  340 LEU
Chi-restraints excluded: chain I residue  333 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:   30.0000
   chunk 33 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 32 optimal weight:   40.0000
   chunk 15 optimal weight:   20.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 344 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 = 0.4377 r_free = 0.4377 target = 0.168431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.121285 restraints weight = 5663.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.125141 restraints weight = 2766.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.127581 restraints weight = 1819.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2780  Z= 0.200
  Angle     :  0.806   8.998   3725  Z= 0.416
  Chirality :  0.045   0.157    375
  Planarity :  0.006   0.053    505
  Dihedral  :  6.673  23.599    375
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 22.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.98 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.23 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.98 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP H 334 
 PHE   0.027   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04631 (   44)
  hydrogen bonds       : angle      10.17968 (  132)
  covalent geometry    : bond        0.00458 ( 2780)
  covalent geometry    : angle       0.80637 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.324 
Fit side-chains
REVERT: D  316 PHE cc_start: 0.7616 (p90) cc_final: 0.5839 (m-80)
REVERT: D  319 ASN cc_start: 0.8584 (p0) cc_final: 0.8283 (p0)
REVERT: D  322 MET cc_start: 0.8281 (mtt) cc_final: 0.8045 (mtt)
REVERT: D  334 TRP cc_start: 0.7700 (p-90) cc_final: 0.4156 (m100)
REVERT: D  337 MET cc_start: 0.7415 (ptp) cc_final: 0.5906 (mmp)
REVERT: D  344 GLN cc_start: 0.7584 (pt0) cc_final: 0.7227 (tt0)
REVERT: E  337 MET cc_start: 0.7606 (ttm) cc_final: 0.7238 (mtp)
REVERT: E  344 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7774 (tt0)
REVERT: F  323 MET cc_start: 0.6276 (ttp) cc_final: 0.4809 (mtt)
REVERT: H  319 ASN cc_start: 0.8554 (p0) cc_final: 0.8346 (t0)
REVERT: I  323 MET cc_start: 0.7116 (ptm) cc_final: 0.6563 (ptm)
REVERT: I  339 MET cc_start: 0.7797 (mpt) cc_final: 0.7073 (mpt)
  outliers start: 10
  outliers final: 2
  residues processed: 95
  average time/residue: 0.1134
  time to fit residues: 13.5465
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  344 GLN
Chi-restraints excluded: chain I residue  333 SER
Chi-restraints excluded: chain I residue  344 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 32 optimal weight:   30.0000
   chunk 4 optimal weight:    6.9990
   chunk 7 optimal weight:   30.0000
   chunk 5 optimal weight:    7.9990
   chunk 18 optimal weight:   40.0000
   chunk 10 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 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 = 0.4418 r_free = 0.4418 target = 0.175708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.123254 restraints weight = 5665.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.126687 restraints weight = 2737.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.129481 restraints weight = 1863.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2780  Z= 0.168
  Angle     :  0.781   9.310   3725  Z= 0.391
  Chirality :  0.043   0.143    375
  Planarity :  0.006   0.047    505
  Dihedral  :  6.267  21.507    375
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 23.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.60 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.17 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.94 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP J 334 
 PHE   0.023   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (   44)
  hydrogen bonds       : angle       9.79165 (  132)
  covalent geometry    : bond        0.00393 ( 2780)
  covalent geometry    : angle       0.78118 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.308 
Fit side-chains
REVERT: C  323 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6786 (ptp)
REVERT: D  316 PHE cc_start: 0.7690 (p90) cc_final: 0.5717 (m-80)
REVERT: D  319 ASN cc_start: 0.8602 (p0) cc_final: 0.8277 (p0)
REVERT: D  334 TRP cc_start: 0.7644 (p-90) cc_final: 0.4080 (m100)
REVERT: D  337 MET cc_start: 0.7281 (ptp) cc_final: 0.5833 (mmt)
REVERT: F  344 GLN cc_start: 0.7930 (pt0) cc_final: 0.7728 (pt0)
REVERT: G  337 MET cc_start: 0.7259 (ttm) cc_final: 0.7035 (ttm)
REVERT: H  319 ASN cc_start: 0.8620 (p0) cc_final: 0.8388 (t0)
REVERT: I  323 MET cc_start: 0.7105 (ptm) cc_final: 0.6439 (ptm)
  outliers start: 9
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1114
  time to fit residues: 13.0314
Evaluate side-chains
  88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain H residue  330 LEU
Chi-restraints excluded: chain I residue  333 SER
Chi-restraints excluded: chain I residue  344 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 31 optimal weight:   30.0000
   chunk 11 optimal weight:    0.3980
   chunk 32 optimal weight:    0.1980
   chunk 14 optimal weight:   30.0000
   chunk 26 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 8 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   overall best weight:    4.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 GLN
** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 344 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.171647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.125860 restraints weight = 5759.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.130094 restraints weight = 2764.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.131946 restraints weight = 1819.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.4578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2780  Z= 0.152
  Angle     :  0.740   8.028   3725  Z= 0.371
  Chirality :  0.042   0.140    375
  Planarity :  0.005   0.049    505
  Dihedral  :  6.041  20.343    375
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 20.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.25 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.13 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.90 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP J 334 
 PHE   0.022   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03859 (   44)
  hydrogen bonds       : angle       9.54227 (  132)
  covalent geometry    : bond        0.00357 ( 2780)
  covalent geometry    : angle       0.74043 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.388 
Fit side-chains
REVERT: C  323 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7185 (ptp)
REVERT: D  316 PHE cc_start: 0.7489 (p90) cc_final: 0.5680 (m-80)
REVERT: D  319 ASN cc_start: 0.8574 (p0) cc_final: 0.8226 (p0)
REVERT: D  334 TRP cc_start: 0.7630 (p-90) cc_final: 0.3927 (m100)
REVERT: D  337 MET cc_start: 0.7276 (ptp) cc_final: 0.5863 (mmt)
REVERT: D  344 GLN cc_start: 0.7221 (pt0) cc_final: 0.6979 (tt0)
REVERT: G  323 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7011 (ptp)
REVERT: I  323 MET cc_start: 0.6707 (ptm) cc_final: 0.6169 (ptm)
  outliers start: 8
  outliers final: 2
  residues processed: 94
  average time/residue: 0.1070
  time to fit residues: 12.7019
Evaluate side-chains
  89 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain I residue  333 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:   40.0000
   chunk 7 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:   30.0000
   chunk 23 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 319 ASN
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.181874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.133265 restraints weight = 5762.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.137136 restraints weight = 2761.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.139662 restraints weight = 1815.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2780  Z= 0.140
  Angle     :  0.714   8.279   3725  Z= 0.357
  Chirality :  0.040   0.136    375
  Planarity :  0.005   0.054    505
  Dihedral  :  5.840  19.187    375
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 19.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.23 %
    Favored  : 88.77 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.49 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.12 (0.22), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 334 
 PHE   0.021   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (   44)
  hydrogen bonds       : angle       9.37568 (  132)
  covalent geometry    : bond        0.00320 ( 2780)
  covalent geometry    : angle       0.71388 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.278 
Fit side-chains
REVERT: B  316 PHE cc_start: 0.8102 (p90) cc_final: 0.7881 (p90)
REVERT: C  323 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6806 (ptp)
REVERT: D  319 ASN cc_start: 0.8622 (p0) cc_final: 0.8327 (p0)
REVERT: D  337 MET cc_start: 0.7392 (ptp) cc_final: 0.5928 (mmt)
REVERT: F  344 GLN cc_start: 0.8265 (pt0) cc_final: 0.7957 (pt0)
REVERT: G  323 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6532 (ptp)
REVERT: H  322 MET cc_start: 0.8373 (mtm) cc_final: 0.7961 (mtm)
REVERT: I  323 MET cc_start: 0.6160 (ptm) cc_final: 0.5651 (ptp)
  outliers start: 9
  outliers final: 2
  residues processed: 94
  average time/residue: 0.1147
  time to fit residues: 13.4998
Evaluate side-chains
  88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain I residue  333 SER
Chi-restraints excluded: chain I residue  344 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    0.0570
   chunk 3 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:   30.0000
   chunk 0 optimal weight:    5.9990
   overall best weight:    4.3304

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 319 ASN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.185828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.133282 restraints weight = 5903.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.137207 restraints weight = 2829.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.139752 restraints weight = 1888.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.5187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2780  Z= 0.155
  Angle     :  0.736   7.750   3725  Z= 0.364
  Chirality :  0.040   0.136    375
  Planarity :  0.005   0.053    505
  Dihedral  :  5.679  18.859    375
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 20.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.23 %
    Favored  : 88.77 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.62 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.15 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP A 334 
 PHE   0.020   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03517 (   44)
  hydrogen bonds       : angle       9.37957 (  132)
  covalent geometry    : bond        0.00370 ( 2780)
  covalent geometry    : angle       0.73598 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A  334 TRP cc_start: 0.5252 (m-90) cc_final: 0.4746 (m-90)
REVERT: C  323 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6814 (ptp)
REVERT: D  319 ASN cc_start: 0.8551 (p0) cc_final: 0.8271 (p0)
REVERT: D  337 MET cc_start: 0.7417 (ptp) cc_final: 0.5772 (mmt)
REVERT: G  323 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6573 (ptp)
REVERT: H  331 GLN cc_start: 0.8232 (tt0) cc_final: 0.7971 (tt0)
REVERT: H  334 TRP cc_start: 0.8839 (p-90) cc_final: 0.8458 (p-90)
REVERT: I  323 MET cc_start: 0.6382 (ptm) cc_final: 0.5733 (ptt)
  outliers start: 7
  outliers final: 4
  residues processed: 89
  average time/residue: 0.1105
  time to fit residues: 12.3710
Evaluate side-chains
  89 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain H residue  316 PHE
Chi-restraints excluded: chain H residue  343 GLN
Chi-restraints excluded: chain I residue  333 SER
Chi-restraints excluded: chain I residue  344 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:   30.0000
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0870
   chunk 4 optimal weight:   20.0000
   chunk 20 optimal weight:   40.0000
   chunk 17 optimal weight:   30.0000
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   overall best weight:    3.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.177066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.133403 restraints weight = 6027.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.137198 restraints weight = 3182.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.139467 restraints weight = 2156.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.5393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2780  Z= 0.146
  Angle     :  0.724   7.620   3725  Z= 0.359
  Chirality :  0.040   0.136    375
  Planarity :  0.005   0.059    505
  Dihedral  :  5.512  18.221    375
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.13 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.11 (0.22), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.17), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 334 
 PHE   0.021   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03284 (   44)
  hydrogen bonds       : angle       9.20849 (  132)
  covalent geometry    : bond        0.00350 ( 2780)
  covalent geometry    : angle       0.72355 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.343 
Fit side-chains
REVERT: D  319 ASN cc_start: 0.8551 (p0) cc_final: 0.8228 (p0)
REVERT: D  330 LEU cc_start: 0.5041 (tp) cc_final: 0.4830 (tp)
REVERT: D  337 MET cc_start: 0.7163 (ptp) cc_final: 0.5762 (mmt)
REVERT: G  323 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7132 (ptp)
REVERT: H  334 TRP cc_start: 0.8742 (p-90) cc_final: 0.8425 (p-90)
REVERT: I  323 MET cc_start: 0.6858 (ptm) cc_final: 0.6308 (ptm)
  outliers start: 7
  outliers final: 2
  residues processed: 88
  average time/residue: 0.1125
  time to fit residues: 12.5250
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain H residue  316 PHE
Chi-restraints excluded: chain H residue  339 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 7 optimal weight:   30.0000
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:   30.0000
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:   30.0000
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 13 optimal weight:    8.9990
   chunk 27 optimal weight:   40.0000
   chunk 16 optimal weight:    5.9990
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 319 ASN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 343 GLN
J 344 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.168924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.127384 restraints weight = 6021.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.130729 restraints weight = 3236.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.132723 restraints weight = 2262.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2780  Z= 0.186
  Angle     :  0.769   7.804   3725  Z= 0.382
  Chirality :  0.041   0.140    375
  Planarity :  0.005   0.063    505
  Dihedral  :  5.702  19.788    375
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 22.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 20.38 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.09 (0.22), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.17), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP J 334 
 PHE   0.020   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (   44)
  hydrogen bonds       : angle       9.13186 (  132)
  covalent geometry    : bond        0.00445 ( 2780)
  covalent geometry    : angle       0.76900 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C  323 MET cc_start: 0.6876 (ptm) cc_final: 0.6675 (ptp)
REVERT: D  319 ASN cc_start: 0.8587 (p0) cc_final: 0.8256 (p0)
REVERT: D  330 LEU cc_start: 0.5366 (tp) cc_final: 0.5162 (tp)
REVERT: D  337 MET cc_start: 0.7152 (ptp) cc_final: 0.5832 (mmt)
REVERT: F  330 LEU cc_start: 0.7814 (tp) cc_final: 0.7417 (tp)
REVERT: H  334 TRP cc_start: 0.8816 (p-90) cc_final: 0.8526 (p-90)
REVERT: I  323 MET cc_start: 0.7208 (ptm) cc_final: 0.6669 (ptm)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 0.1041
  time to fit residues: 10.8520
Evaluate side-chains
  83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain H residue  316 PHE
Chi-restraints excluded: chain H residue  339 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 11 optimal weight:    0.0870
   chunk 12 optimal weight:    6.9990
   chunk 14 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 32 optimal weight:   30.0000
   chunk 1 optimal weight:    0.4980
   chunk 16 optimal weight:   10.0000
   overall best weight:    5.5168

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 343 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.173120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.141766 restraints weight = 5974.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.145979 restraints weight = 2917.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.148732 restraints weight = 1967.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2780  Z= 0.173
  Angle     :  0.764   8.023   3725  Z= 0.376
  Chirality :  0.040   0.138    375
  Planarity :  0.005   0.060    505
  Dihedral  :  5.737  19.121    375
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 21.13 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.15 (0.22), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.17), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 334 
 PHE   0.021   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (   44)
  hydrogen bonds       : angle       8.99629 (  132)
  covalent geometry    : bond        0.00413 ( 2780)
  covalent geometry    : angle       0.76412 ( 3725)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.313 
Fit side-chains
REVERT: D  319 ASN cc_start: 0.8537 (p0) cc_final: 0.8276 (p0)
REVERT: D  337 MET cc_start: 0.7353 (ptp) cc_final: 0.5964 (mmt)
REVERT: H  322 MET cc_start: 0.8182 (ptp) cc_final: 0.7963 (ptp)
REVERT: H  334 TRP cc_start: 0.8933 (p-90) cc_final: 0.8518 (p-90)
REVERT: I  323 MET cc_start: 0.6671 (ptm) cc_final: 0.6225 (ptm)
  outliers start: 3
  outliers final: 2
  residues processed: 82
  average time/residue: 0.1135
  time to fit residues: 11.8334
Evaluate side-chains
  81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain H residue  339 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 4 optimal weight:   30.0000
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 13 optimal weight:   30.0000
   overall best weight:    4.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.177344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.126843 restraints weight = 5711.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.130969 restraints weight = 2670.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.133596 restraints weight = 1762.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.5624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2780  Z= 0.152
  Angle     :  0.735   7.663   3725  Z= 0.362
  Chirality :  0.040   0.135    375
  Planarity :  0.005   0.062    505
  Dihedral  :  5.572  18.466    375
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 18.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 20.75 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.13 (0.22), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.90 (0.17), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 334 
 PHE   0.022   0.002   PHE F 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03274 (   44)
  hydrogen bonds       : angle       8.87739 (  132)
  covalent geometry    : bond        0.00365 ( 2780)
  covalent geometry    : angle       0.73518 ( 3725)

===============================================================================
Job complete
usr+sys time: 1191.87 seconds
wall clock time: 21 minutes 27.76 seconds (1287.76 seconds total)