Starting phenix.real_space_refine
on Wed Mar  5 23:09:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wlj_37621/03_2025/8wlj_37621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wlj_37621/03_2025/8wlj_37621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wlj_37621/03_2025/8wlj_37621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wlj_37621/03_2025/8wlj_37621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wlj_37621/03_2025/8wlj_37621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wlj_37621/03_2025/8wlj_37621.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.073
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      36      5.16       5
     C    2626      2.51       5
     N     662      2.21       5
     O     711      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4035
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3106
          Classifications: {'peptide': 409}
          Link IDs: {'PTRANS': 23, 'TRANS': 385}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 929
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 3.08, per 1000 atoms: 0.76
  Number of scatterers: 4035
  At special positions: 0
  Unit cell: (82.948, 81.084, 103.452, 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      36     16.00
     O     711      8.00
     N     662      7.00
     C    2626      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D 100 " distance=2.04

  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: 0.99
  Conformation dependent library (CDL) restraints added in 505.0 milliseconds
  

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  958

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      73.0% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 54
      removed outlier: 3.840A  pdb=" N   LEU A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      Proline residue:  A  45  - end of helix
    Processing helix  chain 'A' and resid 124 through 157
      removed outlier: 4.784A  pdb=" N   VAL A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   GLY A 132 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
      removed outlier: 3.939A  pdb=" N   ASN A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 179
      removed outlier: 3.566A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
      removed outlier: 4.007A  pdb=" N   MET A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 246
      Proline residue:  A 236  - end of helix
      removed outlier: 3.730A  pdb=" N   LEU A 242 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 270
      removed outlier: 3.713A  pdb=" N   VAL A 254 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A 255 " --> pdb=" O   PRO A 251 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.601A  pdb=" N   LEU A 288 " --> pdb=" O   PRO A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 324
      removed outlier: 3.926A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
      Proline residue:  A 316  - end of helix
      removed outlier: 3.774A  pdb=" N   CYS A 324 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 356
      removed outlier: 4.167A  pdb=" N   VAL A 332 " --> pdb=" O   TRP A 328 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
      removed outlier: 3.659A  pdb=" N   ASN A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLY A 349 " --> pdb=" O   THR A 345 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ILE A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   HIS A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 378
      Proline residue:  A 376  - end of helix
    Processing helix  chain 'A' and resid 380 through 414
      removed outlier: 4.252A  pdb=" N   ALA A 386 " --> pdb=" O   TYR A 382 " (cutoff:3.500A)
      Proline residue:  A 387  - end of helix
      Proline residue:  A 404  - end of helix
      removed outlier: 4.408A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 436
      removed outlier: 4.022A  pdb=" N   GLY A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   TYR A 433 " --> pdb=" O   PHE A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 447
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 3.537A  pdb=" N   PHE A 469 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 487
    Processing helix  chain 'D' and resid 30 through 37
    Processing helix  chain 'D' and resid 91 through 95
      removed outlier: 4.044A  pdb=" N   THR D  95 " --> pdb=" O   PRO D  92 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 7 through 9
      removed outlier: 3.542A  pdb=" N   SER D  23 " --> pdb=" O   SER D   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 14
      removed outlier: 3.922A  pdb=" N   GLY D  12 " --> pdb=" O   GLN D 119 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   THR D 121 " --> pdb=" O   GLY D  12 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   VAL D  14 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS D 101 " --> pdb=" O   GLY D  40 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ALA D  54 " --> pdb=" O   TRP D  41 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    822 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 634
        1.31 -     1.44: 1083
        1.44 -     1.56: 2344
        1.56 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 4123
  Sorted by residual:
  bond pdb=" CA  ALA A 177 "
       pdb=" C   ALA A 177 "
    ideal  model  delta    sigma   weight residual
    1.524  1.424  0.101 1.29e-02 6.01e+03 6.09e+01
  bond pdb=" CA  PHE A 176 "
       pdb=" C   PHE A 176 "
    ideal  model  delta    sigma   weight residual
    1.523  1.452  0.071 1.30e-02 5.92e+03 3.02e+01
  bond pdb=" CA  ALA A 177 "
       pdb=" CB  ALA A 177 "
    ideal  model  delta    sigma   weight residual
    1.530  1.452  0.078 1.63e-02 3.76e+03 2.28e+01
  bond pdb=" C   PHE A 176 "
       pdb=" O   PHE A 176 "
    ideal  model  delta    sigma   weight residual
    1.237  1.184  0.053 1.17e-02 7.31e+03 2.04e+01
  bond pdb=" CA  PHE A 178 "
       pdb=" C   PHE A 178 "
    ideal  model  delta    sigma   weight residual
    1.522  1.460  0.062 1.41e-02 5.03e+03 1.92e+01
  ... (remaining 4118 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 5448
        2.10 -     4.20: 103
        4.20 -     6.31: 35
        6.31 -     8.41: 6
        8.41 -    10.51: 3
  Bond angle restraints: 5595
  Sorted by residual:
  angle pdb=" N   PHE A 178 "
        pdb=" CA  PHE A 178 "
        pdb=" C   PHE A 178 "
      ideal   model   delta    sigma   weight residual
     112.38  101.87   10.51 1.22e+00 6.72e-01 7.42e+01
  angle pdb=" N   SER A 179 "
        pdb=" CA  SER A 179 "
        pdb=" C   SER A 179 "
      ideal   model   delta    sigma   weight residual
     110.24  119.75   -9.51 1.41e+00 5.03e-01 4.55e+01
  angle pdb=" C   SER A 179 "
        pdb=" CA  SER A 179 "
        pdb=" CB  SER A 179 "
      ideal   model   delta    sigma   weight residual
     109.70  101.57    8.13 1.61e+00 3.86e-01 2.55e+01
  angle pdb=" C   PHE A 176 "
        pdb=" N   ALA A 177 "
        pdb=" CA  ALA A 177 "
      ideal   model   delta    sigma   weight residual
     120.71  114.49    6.22 1.67e+00 3.59e-01 1.39e+01
  angle pdb=" N   GLY A 235 "
        pdb=" CA  GLY A 235 "
        pdb=" C   GLY A 235 "
      ideal   model   delta    sigma   weight residual
     112.34  118.79   -6.45 2.04e+00 2.40e-01 1.00e+01
  ... (remaining 5590 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 2201
       17.97 -    35.93: 200
       35.93 -    53.89: 32
       53.89 -    71.86: 4
       71.86 -    89.82: 4
  Dihedral angle restraints: 2441
    sinusoidal: 938
      harmonic: 1503
  Sorted by residual:
  dihedral pdb=" C   SER A 179 "
           pdb=" N   SER A 179 "
           pdb=" CA  SER A 179 "
           pdb=" CB  SER A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.09   -9.51     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" CA  MET D  82 "
           pdb=" C   MET D  82 "
           pdb=" N   VAL D  83 "
           pdb=" CA  VAL D  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.50   17.50     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  GLU D  58 "
           pdb=" C   GLU D  58 "
           pdb=" N   ARG D  59 "
           pdb=" CA  ARG D  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.99   17.01     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 2438 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 589
       0.084 -    0.168: 58
       0.168 -    0.252: 2
       0.252 -    0.335: 0
       0.335 -    0.419: 1
  Chirality restraints: 650
  Sorted by residual:
  chirality pdb=" CA  ALA A 177 "
            pdb=" N   ALA A 177 "
            pdb=" C   ALA A 177 "
            pdb=" CB  ALA A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.42 2.00e-01 2.50e+01 4.39e+00
  chirality pdb=" CA  MET A 175 "
            pdb=" N   MET A 175 "
            pdb=" C   MET A 175 "
            pdb=" CB  MET A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE A 447 "
            pdb=" N   ILE A 447 "
            pdb=" C   ILE A 447 "
            pdb=" CB  ILE A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.65e-01
  ... (remaining 647 not shown)

  Planarity restraints: 702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 174 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   ILE A 174 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ILE A 174 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   MET A 175 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 175 "   -0.015 2.00e-02 2.50e+03   2.89e-02 8.34e+00
        pdb=" C   MET A 175 "    0.050 2.00e-02 2.50e+03
        pdb=" O   MET A 175 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A 176 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 312 "   -0.038 5.00e-02 4.00e+02   5.78e-02 5.35e+00
        pdb=" N   PRO A 313 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 313 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 313 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 699 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 1083
        2.81 -     3.33: 4121
        3.33 -     3.85: 6494
        3.85 -     4.38: 7142
        4.38 -     4.90: 12510
  Nonbonded interactions: 31350
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG D  71 "
            pdb=" O   ASN D  89 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" NH1 ARG D  50 "
            pdb=" O   VAL D  51 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH2 ARG A 413 "
            pdb=" OE2 GLU A 479 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" O   ILE A 301 "
            pdb=" ND2 ASN A 305 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OE2 GLU D   8 "
            pdb=" N   GLY D 117 "
     model   vdw
     2.343 3.120
  ... (remaining 31345 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.770
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
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      :  0.005   0.101   4123  Z= 0.314
  Angle     :  0.817  10.510   5595  Z= 0.431
  Chirality :  0.050   0.419    650
  Planarity :  0.006   0.073    702
  Dihedral  : 14.045  89.824   1480
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.21 %
  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:  0.69 (0.36), residues: 524
  helix:  1.05 (0.27), residues: 345
  sheet:  0.34 (0.89), residues: 42
  loop : -0.87 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 414 
 PHE   0.026   0.002   PHE A 334 
 TYR   0.017   0.002   TYR A 422 
 ARG   0.006   0.001   ARG D  65 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7930 (mm-30)
REVERT: A  142 GLN cc_start: 0.8781 (tt0) cc_final: 0.8303 (tt0)
REVERT: A  167 CYS cc_start: 0.7872 (m) cc_final: 0.7362 (p)
REVERT: A  186 LEU cc_start: 0.8206 (mm) cc_final: 0.7785 (mm)
REVERT: A  354 LYS cc_start: 0.8020 (tttm) cc_final: 0.7728 (tttp)
REVERT: A  426 ASP cc_start: 0.8236 (t70) cc_final: 0.7856 (t70)
REVERT: D   59 ARG cc_start: 0.8956 (mmm-85) cc_final: 0.8645 (mmm-85)
REVERT: D   77 ASP cc_start: 0.7299 (m-30) cc_final: 0.6887 (m-30)
REVERT: D  114 TRP cc_start: 0.7573 (m-10) cc_final: 0.7047 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1560
  time to fit residues: 29.8443
Evaluate side-chains
  132 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 146 ASN
A 329 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.184035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.144682 restraints weight = 6910.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.148784 restraints weight = 3773.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.151543 restraints weight = 2478.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4123  Z= 0.193
  Angle     :  0.659   7.324   5595  Z= 0.331
  Chirality :  0.044   0.157    650
  Planarity :  0.005   0.063    702
  Dihedral  :  4.399  15.935    570
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.58 %
    Favored  : 83.80 %
  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:  0.92 (0.37), residues: 524
  helix:  1.42 (0.27), residues: 346
  sheet: -0.49 (0.80), residues: 50
  loop : -1.06 (0.51), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 328 
 HIS   0.002   0.001   HIS D 101 
 PHE   0.015   0.002   PHE A 334 
 TYR   0.020   0.001   TYR A 182 
 ARG   0.005   0.000   ARG D  50 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8351 (mp) cc_final: 0.7878 (mm)
REVERT: A  138 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8466 (tttp)
REVERT: A  167 CYS cc_start: 0.7784 (m) cc_final: 0.7257 (p)
REVERT: A  178 PHE cc_start: 0.7117 (t80) cc_final: 0.6876 (t80)
REVERT: A  243 TYR cc_start: 0.8337 (t80) cc_final: 0.8136 (t80)
REVERT: A  305 ASN cc_start: 0.8414 (m-40) cc_final: 0.8186 (m110)
REVERT: A  354 LYS cc_start: 0.8058 (tttm) cc_final: 0.7740 (tttp)
REVERT: A  426 ASP cc_start: 0.8490 (t70) cc_final: 0.7872 (t70)
REVERT: A  462 LEU cc_start: 0.8490 (mm) cc_final: 0.8167 (mm)
REVERT: D   77 ASP cc_start: 0.7501 (m-30) cc_final: 0.7117 (m-30)
REVERT: D  114 TRP cc_start: 0.7431 (m-10) cc_final: 0.6785 (m-10)
  outliers start: 7
  outliers final: 5
  residues processed: 142
  average time/residue: 0.1754
  time to fit residues: 30.2907
Evaluate side-chains
  132 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   83 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0170
   chunk 44 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 192 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.184061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.144488 restraints weight = 6879.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.148667 restraints weight = 3767.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.151186 restraints weight = 2457.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4123  Z= 0.181
  Angle     :  0.620   7.275   5595  Z= 0.310
  Chirality :  0.043   0.163    650
  Planarity :  0.005   0.047    702
  Dihedral  :  4.248  13.300    570
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.98 %
    Favored  : 78.70 %
  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:  1.16 (0.37), residues: 524
  helix:  1.61 (0.28), residues: 344
  sheet: -0.40 (0.79), residues: 50
  loop : -0.98 (0.52), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D 101 
 PHE   0.017   0.002   PHE A 176 
 TYR   0.012   0.001   TYR A 422 
 ARG   0.005   0.000   ARG A 189 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   22 ILE cc_start: 0.8266 (mp) cc_final: 0.7927 (mm)
REVERT: A  127 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7428 (mm-30)
REVERT: A  176 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8396 (t80)
REVERT: A  178 PHE cc_start: 0.7228 (t80) cc_final: 0.6950 (t80)
REVERT: A  186 LEU cc_start: 0.8356 (mm) cc_final: 0.8090 (mm)
REVERT: A  354 LYS cc_start: 0.8053 (tttm) cc_final: 0.7816 (tttp)
REVERT: A  430 CYS cc_start: 0.7329 (t) cc_final: 0.6877 (t)
REVERT: A  462 LEU cc_start: 0.8461 (mm) cc_final: 0.8147 (mm)
REVERT: D   77 ASP cc_start: 0.7488 (m-30) cc_final: 0.7097 (m-30)
REVERT: D  114 TRP cc_start: 0.7517 (m-10) cc_final: 0.6910 (m-10)
  outliers start: 10
  outliers final: 8
  residues processed: 144
  average time/residue: 0.1728
  time to fit residues: 30.6562
Evaluate side-chains
  138 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 PHE
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0570
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0570
   overall best weight:    0.5016

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 142 GLN
A 146 ASN
A 329 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.185133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.145948 restraints weight = 6943.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.150206 restraints weight = 3796.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.152761 restraints weight = 2479.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4123  Z= 0.166
  Angle     :  0.632  10.323   5595  Z= 0.312
  Chirality :  0.043   0.169    650
  Planarity :  0.004   0.039    702
  Dihedral  :  4.165  14.153    570
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.91 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.38), residues: 524
  helix:  1.68 (0.28), residues: 344
  sheet: -0.36 (0.80), residues: 50
  loop : -0.88 (0.53), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 328 
 HIS   0.003   0.001   HIS D 101 
 PHE   0.015   0.001   PHE A 348 
 TYR   0.019   0.001   TYR A 182 
 ARG   0.004   0.000   ARG A 413 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8251 (mp) cc_final: 0.7958 (mm)
REVERT: A   28 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8713 (tt)
REVERT: A  127 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7483 (mm-30)
REVERT: A  134 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7951 (mm)
REVERT: A  176 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (t80)
REVERT: A  178 PHE cc_start: 0.7254 (t80) cc_final: 0.6950 (t80)
REVERT: A  186 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8132 (mm)
REVERT: A  305 ASN cc_start: 0.8477 (m-40) cc_final: 0.8234 (m110)
REVERT: A  354 LYS cc_start: 0.8022 (tttm) cc_final: 0.7674 (tttp)
REVERT: A  397 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.7022 (ttm)
REVERT: A  462 LEU cc_start: 0.8425 (mm) cc_final: 0.8109 (mm)
REVERT: D   77 ASP cc_start: 0.7462 (m-30) cc_final: 0.7087 (m-30)
REVERT: D  114 TRP cc_start: 0.7599 (m-10) cc_final: 0.6948 (m-10)
  outliers start: 15
  outliers final: 6
  residues processed: 158
  average time/residue: 0.1544
  time to fit residues: 30.5505
Evaluate side-chains
  150 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  176 PHE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  329 GLN
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 29 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.184913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.145322 restraints weight = 7129.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.149584 restraints weight = 3867.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.152169 restraints weight = 2522.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4123  Z= 0.183
  Angle     :  0.637  10.069   5595  Z= 0.312
  Chirality :  0.043   0.173    650
  Planarity :  0.004   0.035    702
  Dihedral  :  4.122  12.837    570
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.38 %
    Favored  : 72.45 %
  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:  1.36 (0.38), residues: 524
  helix:  1.70 (0.28), residues: 343
  sheet: -0.20 (0.81), residues: 50
  loop : -0.69 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 328 
 HIS   0.002   0.001   HIS D 101 
 PHE   0.016   0.001   PHE A 348 
 TYR   0.016   0.001   TYR A 182 
 ARG   0.003   0.000   ARG A 189 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8222 (mp) cc_final: 0.7928 (mm)
REVERT: A  127 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7471 (mm-30)
REVERT: A  134 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7939 (mm)
REVERT: A  142 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8193 (tt0)
REVERT: A  178 PHE cc_start: 0.7252 (t80) cc_final: 0.6996 (t80)
REVERT: A  186 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8113 (mm)
REVERT: A  305 ASN cc_start: 0.8485 (m-40) cc_final: 0.8201 (m110)
REVERT: A  354 LYS cc_start: 0.8014 (tttm) cc_final: 0.7765 (tttp)
REVERT: A  397 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7030 (ttm)
REVERT: A  462 LEU cc_start: 0.8439 (mm) cc_final: 0.8143 (mm)
REVERT: D   77 ASP cc_start: 0.7488 (m-30) cc_final: 0.7118 (m-30)
REVERT: D  114 TRP cc_start: 0.7617 (m-10) cc_final: 0.6949 (m-10)
  outliers start: 18
  outliers final: 8
  residues processed: 155
  average time/residue: 0.1560
  time to fit residues: 30.2645
Evaluate side-chains
  148 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  142 GLN
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 42 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
A 192 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.183386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.144219 restraints weight = 7002.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.148351 restraints weight = 3838.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151085 restraints weight = 2520.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4123  Z= 0.213
  Angle     :  0.646   9.732   5595  Z= 0.319
  Chirality :  0.043   0.180    650
  Planarity :  0.004   0.043    702
  Dihedral  :  4.129  15.220    570
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.23 %
    Favored  : 71.06 %
  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:  1.26 (0.38), residues: 524
  helix:  1.61 (0.28), residues: 343
  sheet: -0.12 (0.82), residues: 50
  loop : -0.75 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 328 
 HIS   0.002   0.001   HIS D 101 
 PHE   0.016   0.001   PHE A 348 
 TYR   0.020   0.001   TYR A 182 
 ARG   0.005   0.000   ARG A 413 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8248 (mp) cc_final: 0.7959 (mm)
REVERT: A  127 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7525 (mm-30)
REVERT: A  134 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7952 (mm)
REVERT: A  142 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8229 (tt0)
REVERT: A  178 PHE cc_start: 0.7328 (t80) cc_final: 0.7034 (t80)
REVERT: A  186 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8070 (mm)
REVERT: A  305 ASN cc_start: 0.8494 (m-40) cc_final: 0.8176 (m110)
REVERT: A  354 LYS cc_start: 0.8012 (tttm) cc_final: 0.7749 (tttp)
REVERT: A  426 ASP cc_start: 0.8519 (t70) cc_final: 0.7927 (t70)
REVERT: A  462 LEU cc_start: 0.8424 (mm) cc_final: 0.8141 (mm)
REVERT: D   77 ASP cc_start: 0.7529 (m-30) cc_final: 0.7165 (m-30)
REVERT: D  114 TRP cc_start: 0.7648 (m-10) cc_final: 0.6984 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 148
  average time/residue: 0.1638
  time to fit residues: 29.9681
Evaluate side-chains
  152 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  142 GLN
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   chunk 13 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.184188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.145619 restraints weight = 7011.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.149832 restraints weight = 3830.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.152489 restraints weight = 2494.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4123  Z= 0.211
  Angle     :  0.677   9.601   5595  Z= 0.329
  Chirality :  0.045   0.195    650
  Planarity :  0.004   0.036    702
  Dihedral  :  4.133  14.408    570
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 25.00 %
    Favored  : 71.06 %
  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:  1.25 (0.38), residues: 524
  helix:  1.59 (0.28), residues: 343
  sheet: -0.20 (0.82), residues: 50
  loop : -0.70 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 328 
 HIS   0.001   0.000   HIS D 101 
 PHE   0.015   0.001   PHE A 348 
 TYR   0.020   0.001   TYR A 182 
 ARG   0.003   0.000   ARG A 413 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8235 (mp) cc_final: 0.7968 (mm)
REVERT: A  127 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7696 (mm-30)
REVERT: A  178 PHE cc_start: 0.7337 (t80) cc_final: 0.7051 (t80)
REVERT: A  186 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8139 (mm)
REVERT: A  305 ASN cc_start: 0.8464 (m-40) cc_final: 0.8149 (m110)
REVERT: A  354 LYS cc_start: 0.7981 (tttm) cc_final: 0.7719 (tttp)
REVERT: A  462 LEU cc_start: 0.8438 (mm) cc_final: 0.8159 (mm)
REVERT: D   77 ASP cc_start: 0.7493 (m-30) cc_final: 0.7109 (m-30)
REVERT: D  114 TRP cc_start: 0.7650 (m-10) cc_final: 0.6970 (m-10)
  outliers start: 17
  outliers final: 11
  residues processed: 152
  average time/residue: 0.1532
  time to fit residues: 29.5224
Evaluate side-chains
  152 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0670
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 47 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0570
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
** A 192 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 = 0.4222 r_free = 0.4222 target = 0.186006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.147317 restraints weight = 6887.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.151473 restraints weight = 3776.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.154236 restraints weight = 2470.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   4123  Z= 0.212
  Angle     :  0.697   9.057   5595  Z= 0.341
  Chirality :  0.045   0.226    650
  Planarity :  0.004   0.052    702
  Dihedral  :  4.110  14.179    570
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 27.08 %
    Favored  : 70.37 %
  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:  1.32 (0.38), residues: 524
  helix:  1.62 (0.28), residues: 343
  sheet: -0.01 (0.82), residues: 49
  loop : -0.65 (0.55), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 328 
 HIS   0.001   0.000   HIS D 101 
 PHE   0.015   0.001   PHE A 348 
 TYR   0.017   0.001   TYR A 182 
 ARG   0.002   0.000   ARG A 413 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8158 (mp) cc_final: 0.7893 (mm)
REVERT: A  127 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: A  178 PHE cc_start: 0.7282 (t80) cc_final: 0.7022 (t80)
REVERT: A  186 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8167 (mm)
REVERT: A  230 MET cc_start: 0.8794 (tmm) cc_final: 0.8536 (tmm)
REVERT: A  305 ASN cc_start: 0.8407 (m-40) cc_final: 0.8117 (m110)
REVERT: A  354 LYS cc_start: 0.7976 (tttm) cc_final: 0.7716 (tttp)
REVERT: A  397 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7075 (ttm)
REVERT: A  462 LEU cc_start: 0.8439 (mm) cc_final: 0.8165 (mm)
REVERT: D   65 ARG cc_start: 0.6964 (ptm160) cc_final: 0.6424 (ptt-90)
REVERT: D   77 ASP cc_start: 0.7474 (m-30) cc_final: 0.7082 (m-30)
REVERT: D  114 TRP cc_start: 0.7617 (m-10) cc_final: 0.6923 (m-10)
  outliers start: 11
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1489
  time to fit residues: 27.9725
Evaluate side-chains
  145 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    0.1980
   chunk 43 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 28 optimal weight:    0.4980
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.186443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.147099 restraints weight = 7034.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.151324 restraints weight = 3816.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.153943 restraints weight = 2487.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   4123  Z= 0.201
  Angle     :  0.683   8.731   5595  Z= 0.333
  Chirality :  0.044   0.218    650
  Planarity :  0.004   0.035    702
  Dihedral  :  4.098  13.206    570
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 27.08 %
    Favored  : 70.14 %
  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:  1.30 (0.38), residues: 524
  helix:  1.64 (0.28), residues: 342
  sheet: -0.00 (0.82), residues: 49
  loop : -0.76 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP A 328 
 HIS   0.001   0.000   HIS D 101 
 PHE   0.016   0.001   PHE A 348 
 TYR   0.017   0.001   TYR A 182 
 ARG   0.001   0.000   ARG A 189 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8128 (mp) cc_final: 0.7873 (mm)
REVERT: A  127 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7741 (mm-30)
REVERT: A  178 PHE cc_start: 0.7267 (t80) cc_final: 0.7015 (t80)
REVERT: A  186 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8157 (mm)
REVERT: A  354 LYS cc_start: 0.7966 (tttm) cc_final: 0.7598 (tttp)
REVERT: A  397 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7077 (ttm)
REVERT: D   65 ARG cc_start: 0.6928 (ptm160) cc_final: 0.6381 (ptt-90)
REVERT: D   77 ASP cc_start: 0.7455 (m-30) cc_final: 0.7092 (m-30)
REVERT: D  114 TRP cc_start: 0.7640 (m-10) cc_final: 0.6940 (m-10)
  outliers start: 12
  outliers final: 8
  residues processed: 144
  average time/residue: 0.1440
  time to fit residues: 26.1233
Evaluate side-chains
  146 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0010
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.187096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.147455 restraints weight = 7021.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.151694 restraints weight = 3855.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.154536 restraints weight = 2526.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4123  Z= 0.195
  Angle     :  0.694   8.872   5595  Z= 0.337
  Chirality :  0.044   0.208    650
  Planarity :  0.004   0.035    702
  Dihedral  :  4.078  13.641    570
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 28.24 %
    Favored  : 69.44 %
  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:  1.35 (0.38), residues: 524
  helix:  1.67 (0.28), residues: 341
  sheet:  0.15 (0.83), residues: 49
  loop : -0.77 (0.55), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A 328 
 HIS   0.001   0.000   HIS D 101 
 PHE   0.016   0.001   PHE A 348 
 TYR   0.019   0.002   TYR A 182 
 ARG   0.002   0.000   ARG A 217 

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8098 (mp) cc_final: 0.7875 (mm)
REVERT: A   43 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8069 (tp)
REVERT: A  127 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7705 (mm-30)
REVERT: A  142 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7474 (pp30)
REVERT: A  186 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8133 (mm)
REVERT: A  230 MET cc_start: 0.8772 (tmm) cc_final: 0.8563 (tmm)
REVERT: A  243 TYR cc_start: 0.8228 (t80) cc_final: 0.7993 (t80)
REVERT: A  354 LYS cc_start: 0.7946 (tttm) cc_final: 0.7580 (tttp)
REVERT: A  426 ASP cc_start: 0.8363 (t70) cc_final: 0.7631 (t70)
REVERT: D   77 ASP cc_start: 0.7466 (m-30) cc_final: 0.7108 (m-30)
REVERT: D  114 TRP cc_start: 0.7654 (m-10) cc_final: 0.6955 (m-10)
  outliers start: 10
  outliers final: 5
  residues processed: 143
  average time/residue: 0.1384
  time to fit residues: 25.1533
Evaluate side-chains
  145 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.185453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145387 restraints weight = 7007.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.149498 restraints weight = 3883.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.152219 restraints weight = 2566.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4123  Z= 0.223
  Angle     :  0.698   8.504   5595  Z= 0.341
  Chirality :  0.044   0.193    650
  Planarity :  0.004   0.035    702
  Dihedral  :  4.077  13.673    570
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 28.01 %
    Favored  : 69.44 %
  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:  1.35 (0.38), residues: 524
  helix:  1.62 (0.28), residues: 343
  sheet:  0.18 (0.82), residues: 49
  loop : -0.68 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A 328 
 HIS   0.001   0.000   HIS A 353 
 PHE   0.011   0.001   PHE A 429 
 TYR   0.019   0.002   TYR A 182 
 ARG   0.001   0.000   ARG D  65 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1885.48 seconds
wall clock time: 33 minutes 13.80 seconds (1993.80 seconds total)