Starting phenix.real_space_refine
on Wed Sep 17 03:15:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n3b_9350/09_2025/6n3b_9350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n3b_9350/09_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_9350/09_2025/6n3b_9350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n3b_9350/09_2025/6n3b_9350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n3b_9350/09_2025/6n3b_9350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n3b_9350/09_2025/6n3b_9350.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.55, per 1000 atoms: 0.20
  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: 0.22
  Conformation dependent library (CDL) restraints added in 112.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.14
  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: 0.35

  Time building geometry restraints manager: 0.29 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: 0.01
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:             0.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.540
  Find NCS groups from input model:        0.020
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 PHE   0.035   0.009   PHE F 316 
 TRP   0.019   0.004   TRP D 334 

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

*********************** 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  : 0.099 
Fit side-chains
REVERT: B  334 TRP cc_start: 0.8783 (p-90) cc_final: 0.7832 (p-90)
REVERT: B  342 SER cc_start: 0.8351 (m) cc_final: 0.8001 (p)
REVERT: D  316 PHE cc_start: 0.7542 (p90) cc_final: 0.5863 (m-80)
REVERT: D  334 TRP cc_start: 0.8162 (p-90) cc_final: 0.4015 (t60)
REVERT: D  337 MET cc_start: 0.7292 (ptp) cc_final: 0.5927 (mmp)
REVERT: D  344 GLN cc_start: 0.7142 (pt0) cc_final: 0.6913 (tt0)
REVERT: E  336 MET cc_start: 0.7385 (mtt) cc_final: 0.7115 (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: 0.8044 (p-90)
REVERT: G  323 MET cc_start: 0.7210 (ptm) cc_final: 0.6991 (ptm)
REVERT: H  334 TRP cc_start: 0.8604 (p-90) cc_final: 0.8010 (p-90)
REVERT: H  342 SER cc_start: 0.8294 (m) cc_final: 0.7928 (p)
REVERT: I  323 MET cc_start: 0.7277 (ptm) cc_final: 0.6948 (ptm)
REVERT: I  336 MET cc_start: 0.7279 (mtt) cc_final: 0.7079 (mtt)
REVERT: J  313 PHE cc_start: 0.6858 (m-10) cc_final: 0.6526 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0416
  time to fit residues: 6.4231
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  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:   30.0000
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   overall best weight:    4.5188

-------------------------------------------------------------------------------
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 = 0.4363 r_free = 0.4363 target = 0.171884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.127244 restraints weight = 5920.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.130858 restraints weight = 3015.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.132829 restraints weight = 1971.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.134499 restraints weight = 1543.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.134879 restraints weight = 1289.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2780  Z= 0.168
  Angle     :  0.825  16.101   3725  Z= 0.419
  Chirality :  0.044   0.149    375
  Planarity :  0.006   0.052    505
  Dihedral  :  6.948  22.460    375
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 23.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.58 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.25 (0.22), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.17), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.037   0.003   PHE F 316 
 TRP   0.020   0.002   TRP J 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 2780)
  covalent geometry    : angle       0.82498 ( 3725)
  hydrogen bonds       : bond        0.04744 (   44)
  hydrogen bonds       : angle      10.59379 (  132)

*********************** 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
  111 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: D  316 PHE cc_start: 0.7577 (p90) cc_final: 0.6078 (m-80)
REVERT: D  319 ASN cc_start: 0.8385 (p0) cc_final: 0.8109 (p0)
REVERT: D  334 TRP cc_start: 0.8142 (p-90) cc_final: 0.3583 (m100)
REVERT: D  337 MET cc_start: 0.7236 (ptp) cc_final: 0.5870 (mmp)
REVERT: F  323 MET cc_start: 0.6752 (ttp) cc_final: 0.5259 (mtt)
REVERT: F  334 TRP cc_start: 0.8458 (p-90) cc_final: 0.7767 (p-90)
REVERT: G  323 MET cc_start: 0.7486 (ptm) cc_final: 0.7045 (ptp)
REVERT: I  323 MET cc_start: 0.7317 (ptm) cc_final: 0.6768 (ptm)
REVERT: I  339 MET cc_start: 0.7259 (mpt) cc_final: 0.7012 (mpt)
REVERT: J  313 PHE cc_start: 0.6506 (m-10) cc_final: 0.5778 (p90)
REVERT: J  323 MET cc_start: 0.5336 (ttt) cc_final: 0.4420 (mtp)
REVERT: J  344 GLN cc_start: 0.7755 (pt0) cc_final: 0.7432 (pt0)
  outliers start: 10
  outliers final: 3
  residues processed: 104
  average time/residue: 0.0355
  time to fit residues: 4.7790
Evaluate side-chains
  88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:   40.0000
   chunk 26 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 20 optimal weight:   30.0000
   chunk 34 optimal weight:   30.0000
   chunk 31 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 27 optimal weight:   30.0000
   overall best weight:   17.9998

-------------------------------------------------------------------------------
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 319 ASN
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 344 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 = 0.4242 r_free = 0.4242 target = 0.149216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.120072 restraints weight = 6287.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.123950 restraints weight = 3025.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.126287 restraints weight = 2005.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.127634 restraints weight = 1590.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.128370 restraints weight = 1369.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.060   2780  Z= 0.416
  Angle     :  1.087  10.286   3725  Z= 0.575
  Chirality :  0.051   0.172    375
  Planarity :  0.007   0.056    505
  Dihedral  :  7.938  27.949    375
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 33.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.52 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 14.72 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.29 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.025   0.003   PHE F 316 
 TRP   0.035   0.005   TRP H 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00953 ( 2780)
  covalent geometry    : angle       1.08708 ( 3725)
  hydrogen bonds       : bond        0.06004 (   44)
  hydrogen bonds       : angle      10.54578 (  132)

*********************** 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
  92 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.114 
Fit side-chains
REVERT: C  323 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7290 (ptm)
REVERT: D  319 ASN cc_start: 0.8658 (p0) cc_final: 0.8263 (p0)
REVERT: D  334 TRP cc_start: 0.8168 (p-90) cc_final: 0.4244 (m100)
REVERT: D  337 MET cc_start: 0.7777 (ptp) cc_final: 0.6327 (mmt)
REVERT: E  344 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8084 (tt0)
REVERT: F  323 MET cc_start: 0.6502 (ttp) cc_final: 0.5087 (mtt)
REVERT: G  323 MET cc_start: 0.7491 (ptm) cc_final: 0.6993 (ptm)
REVERT: H  344 GLN cc_start: 0.8233 (pt0) cc_final: 0.7924 (pt0)
REVERT: I  323 MET cc_start: 0.7353 (ptm) cc_final: 0.6981 (ptm)
REVERT: J  313 PHE cc_start: 0.5566 (m-10) cc_final: 0.5007 (p90)
  outliers start: 10
  outliers final: 4
  residues processed: 89
  average time/residue: 0.0442
  time to fit residues: 5.0891
Evaluate side-chains
  82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  337 MET
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain E residue  344 GLN
Chi-restraints excluded: chain G residue  330 LEU
Chi-restraints excluded: chain H residue  340 LEU
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 25 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:   30.0000
   chunk 3 optimal weight:   40.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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**
H 343 GLN
** I 344 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 = 0.4412 r_free = 0.4412 target = 0.171338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.120094 restraints weight = 5846.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.123839 restraints weight = 2892.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.126047 restraints weight = 1910.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.127600 restraints weight = 1514.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.128004 restraints weight = 1301.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.4266

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= 0.190
  Angle     :  0.825   9.697   3725  Z= 0.421
  Chirality :  0.043   0.148    375
  Planarity :  0.006   0.050    505
  Dihedral  :  6.754  22.664    375
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 25.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.28 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.16), residues: 365

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 2780)
  covalent geometry    : angle       0.82497 ( 3725)
  hydrogen bonds       : bond        0.04377 (   44)
  hydrogen bonds       : angle       9.93061 (  132)

*********************** 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
  95 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.093 
Fit side-chains
REVERT: C  323 MET cc_start: 0.7680 (ptm) cc_final: 0.7451 (ptm)
REVERT: D  319 ASN cc_start: 0.8590 (p0) cc_final: 0.8232 (p0)
REVERT: D  334 TRP cc_start: 0.7667 (p-90) cc_final: 0.4021 (m100)
REVERT: D  337 MET cc_start: 0.7439 (ptp) cc_final: 0.6010 (mmp)
REVERT: E  344 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7940 (tt0)
REVERT: G  323 MET cc_start: 0.7300 (ptm) cc_final: 0.6905 (ptp)
REVERT: H  331 GLN cc_start: 0.8130 (tt0) cc_final: 0.7826 (tt0)
REVERT: I  323 MET cc_start: 0.7136 (ptm) cc_final: 0.6657 (ptm)
  outliers start: 9
  outliers final: 2
  residues processed: 90
  average time/residue: 0.0432
  time to fit residues: 5.0525
Evaluate side-chains
  81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  344 GLN
Chi-restraints excluded: chain G residue  322 MET
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 22 optimal weight:    0.0170
   chunk 19 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   chunk 24 optimal weight:   30.0000
   chunk 28 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 16 optimal weight:    4.9990
   overall best weight:    6.4026

-------------------------------------------------------------------------------
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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 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 = 0.4410 r_free = 0.4410 target = 0.175604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.120096 restraints weight = 5908.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.123806 restraints weight = 2895.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.125939 restraints weight = 1910.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.127582 restraints weight = 1512.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.127595 restraints weight = 1289.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2780  Z= 0.192
  Angle     :  0.819   8.616   3725  Z= 0.409
  Chirality :  0.043   0.143    375
  Planarity :  0.006   0.047    505
  Dihedral  :  6.431  23.342    375
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 23.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.70 %
    Favored  : 86.30 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.98 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.19 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.95 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.020   0.002   PHE F 316 
 TRP   0.021   0.003   TRP J 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 2780)
  covalent geometry    : angle       0.81911 ( 3725)
  hydrogen bonds       : bond        0.04106 (   44)
  hydrogen bonds       : angle       9.47796 (  132)

*********************** 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
  94 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.071 
Fit side-chains
REVERT: D  319 ASN cc_start: 0.8631 (p0) cc_final: 0.8268 (p0)
REVERT: D  337 MET cc_start: 0.7503 (ptp) cc_final: 0.6062 (mmp)
REVERT: E  344 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7860 (tt0)
REVERT: F  323 MET cc_start: 0.6537 (ttt) cc_final: 0.4894 (mtt)
REVERT: G  323 MET cc_start: 0.7220 (ptm) cc_final: 0.6994 (ptm)
REVERT: H  331 GLN cc_start: 0.8246 (tt0) cc_final: 0.7951 (tt0)
REVERT: I  323 MET cc_start: 0.6763 (ptm) cc_final: 0.6306 (ptm)
  outliers start: 9
  outliers final: 2
  residues processed: 86
  average time/residue: 0.0430
  time to fit residues: 4.7354
Evaluate side-chains
  79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain E residue  344 GLN
Chi-restraints excluded: chain G residue  322 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 10 optimal weight:   40.0000
   chunk 31 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:   40.0000
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    6.1994

-------------------------------------------------------------------------------
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**
B 344 GLN
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 344 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 = 0.4387 r_free = 0.4387 target = 0.156733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.132095 restraints weight = 5991.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.136438 restraints weight = 2775.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.138762 restraints weight = 1790.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.140798 restraints weight = 1414.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.141319 restraints weight = 1164.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.4854

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= 0.190
  Angle     :  0.792   9.253   3725  Z= 0.398
  Chirality :  0.042   0.148    375
  Planarity :  0.006   0.052    505
  Dihedral  :  6.296  22.037    375
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 21.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.75 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.25 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.020   0.002   PHE F 316 
 TRP   0.018   0.002   TRP J 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 2780)
  covalent geometry    : angle       0.79225 ( 3725)
  hydrogen bonds       : bond        0.03993 (   44)
  hydrogen bonds       : angle       9.46834 (  132)

*********************** 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
  87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.100 
Fit side-chains
REVERT: D  319 ASN cc_start: 0.8621 (p0) cc_final: 0.8248 (p0)
REVERT: D  337 MET cc_start: 0.7303 (ptp) cc_final: 0.6085 (mmt)
REVERT: F  323 MET cc_start: 0.6754 (ttt) cc_final: 0.5088 (mtt)
REVERT: G  323 MET cc_start: 0.7182 (ptm) cc_final: 0.6745 (ptp)
REVERT: I  323 MET cc_start: 0.6765 (ptm) cc_final: 0.6348 (ptm)
  outliers start: 7
  outliers final: 3
  residues processed: 83
  average time/residue: 0.0426
  time to fit residues: 4.5954
Evaluate side-chains
  80 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain G residue  322 MET
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 26 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 327 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 = 0.4461 r_free = 0.4461 target = 0.179209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.122279 restraints weight = 5777.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.126197 restraints weight = 2820.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.128293 restraints weight = 1867.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.129849 restraints weight = 1487.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.131057 restraints weight = 1281.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.5073

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= 0.171
  Angle     :  0.775   7.993   3725  Z= 0.389
  Chirality :  0.042   0.142    375
  Planarity :  0.006   0.060    505
  Dihedral  :  6.130  21.275    375
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 22.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.05 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.38 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.25 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.019   0.002   PHE F 316 
 TRP   0.017   0.002   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 2780)
  covalent geometry    : angle       0.77537 ( 3725)
  hydrogen bonds       : bond        0.03678 (   44)
  hydrogen bonds       : angle       9.46393 (  132)

*********************** 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
  87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  334 TRP cc_start: 0.7571 (OUTLIER) cc_final: 0.7215 (m-90)
REVERT: D  319 ASN cc_start: 0.8620 (p0) cc_final: 0.8241 (p0)
REVERT: D  337 MET cc_start: 0.7278 (ptp) cc_final: 0.6130 (mmt)
REVERT: F  323 MET cc_start: 0.6743 (ttt) cc_final: 0.4992 (mtt)
REVERT: G  323 MET cc_start: 0.7368 (ptm) cc_final: 0.6908 (ptp)
REVERT: I  323 MET cc_start: 0.6765 (ptm) cc_final: 0.6340 (ptm)
  outliers start: 6
  outliers final: 1
  residues processed: 83
  average time/residue: 0.0373
  time to fit residues: 4.0291
Evaluate side-chains
  79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:   30.0000
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:   40.0000
   chunk 20 optimal weight:   20.0000
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 327 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 = 0.4520 r_free = 0.4520 target = 0.178373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.126010 restraints weight = 6002.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.130282 restraints weight = 2814.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.133031 restraints weight = 1841.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.134094 restraints weight = 1430.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.135221 restraints weight = 1271.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.5335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2780  Z= 0.144
  Angle     :  0.715   7.732   3725  Z= 0.362
  Chirality :  0.041   0.137    375
  Planarity :  0.006   0.063    505
  Dihedral  :  5.830  19.459    375
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 21.13 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.17 (0.22), 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
 PHE   0.024   0.002   PHE F 316 
 TRP   0.023   0.002   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2780)
  covalent geometry    : angle       0.71504 ( 3725)
  hydrogen bonds       : bond        0.03304 (   44)
  hydrogen bonds       : angle       9.04186 (  132)

*********************** 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
  89 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  334 TRP cc_start: 0.7455 (OUTLIER) cc_final: 0.7079 (m-90)
REVERT: C  330 LEU cc_start: 0.8806 (tp) cc_final: 0.8393 (mt)
REVERT: D  319 ASN cc_start: 0.8626 (p0) cc_final: 0.8262 (p0)
REVERT: D  337 MET cc_start: 0.7163 (ptp) cc_final: 0.5981 (mmt)
REVERT: G  323 MET cc_start: 0.7196 (ptm) cc_final: 0.6778 (ptp)
REVERT: H  323 MET cc_start: 0.5138 (ttt) cc_final: 0.4048 (mtp)
REVERT: I  323 MET cc_start: 0.6578 (ptm) cc_final: 0.5886 (ptp)
  outliers start: 4
  outliers final: 1
  residues processed: 86
  average time/residue: 0.0429
  time to fit residues: 4.7949
Evaluate side-chains
  82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 0 optimal weight:   40.0000
   chunk 10 optimal weight:   30.0000
   chunk 29 optimal weight:    0.0030
   chunk 12 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    5.5998

-------------------------------------------------------------------------------
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 327 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 = 0.4513 r_free = 0.4513 target = 0.181984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.122583 restraints weight = 5970.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.126582 restraints weight = 2886.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.128958 restraints weight = 1922.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.129826 restraints weight = 1533.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.131260 restraints weight = 1386.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2780  Z= 0.177
  Angle     :  0.766   7.960   3725  Z= 0.386
  Chirality :  0.041   0.138    375
  Planarity :  0.006   0.063    505
  Dihedral  :  5.965  20.084    375
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 21.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.60 %
    Favored  : 87.40 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 21.89 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 PHE   0.021   0.002   PHE B 316 
 TRP   0.018   0.002   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 2780)
  covalent geometry    : angle       0.76633 ( 3725)
  hydrogen bonds       : bond        0.03464 (   44)
  hydrogen bonds       : angle       9.11889 (  132)

*********************** 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
  85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A  334 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.7139 (m-90)
REVERT: C  330 LEU cc_start: 0.8661 (tp) cc_final: 0.8362 (mt)
REVERT: D  319 ASN cc_start: 0.8622 (p0) cc_final: 0.8277 (p0)
REVERT: D  337 MET cc_start: 0.7261 (ptp) cc_final: 0.6058 (mmt)
REVERT: G  323 MET cc_start: 0.7260 (ptm) cc_final: 0.6851 (ptp)
REVERT: I  323 MET cc_start: 0.6727 (ptm) cc_final: 0.6353 (ptm)
  outliers start: 2
  outliers final: 1
  residues processed: 84
  average time/residue: 0.0425
  time to fit residues: 4.6493
Evaluate side-chains
  82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 1 optimal weight:    0.0470
   chunk 32 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 17 optimal weight:   40.0000
   chunk 26 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 18 optimal weight:   50.0000
   chunk 14 optimal weight:   30.0000
   overall best weight:    6.4086

-------------------------------------------------------------------------------
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 327 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 = 0.4484 r_free = 0.4484 target = 0.174518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.121753 restraints weight = 5836.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.125666 restraints weight = 2858.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.127942 restraints weight = 1919.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.129542 restraints weight = 1531.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.129953 restraints weight = 1323.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.5428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2780  Z= 0.192
  Angle     :  0.785   8.168   3725  Z= 0.399
  Chirality :  0.042   0.142    375
  Planarity :  0.006   0.064    505
  Dihedral  :  6.114  20.477    375
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 21.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.60 %
    Favored  : 87.40 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 22.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.28 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.032   0.003   PHE F 316 
 TRP   0.021   0.002   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 2780)
  covalent geometry    : angle       0.78459 ( 3725)
  hydrogen bonds       : bond        0.03556 (   44)
  hydrogen bonds       : angle       9.09913 (  132)

********************** 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
  83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  334 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.7154 (m-90)
REVERT: C  330 LEU cc_start: 0.8649 (tp) cc_final: 0.8395 (mt)
REVERT: D  319 ASN cc_start: 0.8616 (p0) cc_final: 0.8254 (p0)
REVERT: D  337 MET cc_start: 0.7261 (ptp) cc_final: 0.6136 (mmt)
REVERT: G  323 MET cc_start: 0.7351 (ptm) cc_final: 0.6939 (ptp)
REVERT: I  323 MET cc_start: 0.6818 (ptm) cc_final: 0.6419 (ptm)
  outliers start: 3
  outliers final: 1
  residues processed: 81
  average time/residue: 0.0407
  time to fit residues: 4.3346
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  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 21 optimal weight:   30.0000
   chunk 16 optimal weight:   30.0000
   chunk 26 optimal weight:   30.0000
   chunk 2 optimal weight:    5.9990
   chunk 18 optimal weight:   50.0000
   chunk 17 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 33 optimal weight:   30.0000
   chunk 34 optimal weight:    8.9990
   overall best weight:   12.3994

-------------------------------------------------------------------------------
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**
C 319 ASN
F 319 ASN
F 344 GLN
** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 344 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.152218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.123789 restraints weight = 6017.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.127608 restraints weight = 2887.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.129700 restraints weight = 1938.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.131426 restraints weight = 1565.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.132257 restraints weight = 1340.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   2780  Z= 0.311
  Angle     :  0.939   9.708   3725  Z= 0.483
  Chirality :  0.045   0.154    375
  Planarity :  0.006   0.063    505
  Dihedral  :  6.927  23.815    375
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 27.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.16 %
    Favored  : 83.84 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 23.02 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.44 (0.21), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.14 (0.16), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.035   0.003   PHE H 316 
 TRP   0.024   0.003   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 2780)
  covalent geometry    : angle       0.93909 ( 3725)
  hydrogen bonds       : bond        0.04513 (   44)
  hydrogen bonds       : angle       9.36115 (  132)

===============================================================================
Job complete
usr+sys time: 602.83 seconds
wall clock time: 11 minutes 3.97 seconds (663.97 seconds total)