Starting phenix.real_space_refine
on Fri Aug 22 14:20:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wlj_37621/08_2025/8wlj_37621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wlj_37621/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wlj_37621/08_2025/8wlj_37621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wlj_37621/08_2025/8wlj_37621.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wlj_37621/08_2025/8wlj_37621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wlj_37621/08_2025/8wlj_37621.map"
  }
  resolution = 3.6
  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
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.24, per 1000 atoms: 0.31
  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: 0.27
  Conformation dependent library (CDL) restraints added in 93.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.11
  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: 0.67

  Time building geometry restraints manager: 0.35 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.880
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.320
-------------------------------------------------------------------------------
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   4124  Z= 0.316
  Angle     :  0.817  10.510   5597  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 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:  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
 ARG   0.006   0.001   ARG D  65 
 TYR   0.017   0.002   TYR A 422 
 PHE   0.026   0.002   PHE A 334 
 TRP   0.012   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 4123)
  covalent geometry    : angle       0.81736 ( 5595)
  SS BOND              : bond        0.00443 (    1)
  SS BOND              : angle       0.42714 (    2)
  hydrogen bonds       : bond        0.13828 (  283)
  hydrogen bonds       : angle       5.89522 (  822)

*********************** 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  : 0.143 
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: 0.0652
  time to fit residues: 12.5227
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  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.184147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.144605 restraints weight = 7046.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.148787 restraints weight = 3815.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.151565 restraints weight = 2493.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.153110 restraints weight = 1844.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.154436 restraints weight = 1525.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4124  Z= 0.137
  Angle     :  0.660   7.141   5597  Z= 0.332
  Chirality :  0.045   0.157    650
  Planarity :  0.006   0.069    702
  Dihedral  :  4.396  15.922    570
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.35 %
    Favored  : 84.03 %
  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:  0.92 (0.37), residues: 524
  helix:  1.42 (0.27), residues: 346
  sheet: -0.49 (0.80), residues: 50
  loop : -1.05 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 189 
 TYR   0.018   0.001   TYR A 182 
 PHE   0.015   0.002   PHE A 334 
 TRP   0.013   0.001   TRP A 328 
 HIS   0.002   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4123)
  covalent geometry    : angle       0.65953 ( 5595)
  SS BOND              : bond        0.00636 (    1)
  SS BOND              : angle       1.81955 (    2)
  hydrogen bonds       : bond        0.04359 (  283)
  hydrogen bonds       : angle       5.22280 (  822)

*********************** 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  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8339 (mp) cc_final: 0.7858 (mm)
REVERT: A  138 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8447 (tttp)
REVERT: A  167 CYS cc_start: 0.7742 (m) cc_final: 0.7250 (p)
REVERT: A  178 PHE cc_start: 0.7137 (t80) cc_final: 0.6893 (t80)
REVERT: A  243 TYR cc_start: 0.8301 (t80) cc_final: 0.8079 (t80)
REVERT: A  305 ASN cc_start: 0.8399 (m-40) cc_final: 0.8168 (m110)
REVERT: A  354 LYS cc_start: 0.8052 (tttm) cc_final: 0.7738 (tttp)
REVERT: A  426 ASP cc_start: 0.8484 (t70) cc_final: 0.7859 (t70)
REVERT: A  462 LEU cc_start: 0.8475 (mm) cc_final: 0.8152 (mm)
REVERT: D   77 ASP cc_start: 0.7488 (m-30) cc_final: 0.7110 (m-30)
REVERT: D  114 TRP cc_start: 0.7444 (m-10) cc_final: 0.6811 (m-10)
  outliers start: 7
  outliers final: 5
  residues processed: 142
  average time/residue: 0.0689
  time to fit residues: 11.9605
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  : 0.097 
-------------------------------------------------------------------------------
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 33 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.181673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142161 restraints weight = 6927.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.146233 restraints weight = 3794.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.148881 restraints weight = 2492.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.150636 restraints weight = 1858.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.151699 restraints weight = 1523.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4124  Z= 0.147
  Angle     :  0.636   7.503   5597  Z= 0.319
  Chirality :  0.044   0.165    650
  Planarity :  0.005   0.050    702
  Dihedral  :  4.289  13.669    570
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.44 %
    Favored  : 78.01 %
  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:  1.13 (0.37), residues: 524
  helix:  1.59 (0.28), residues: 343
  sheet: -0.42 (0.79), residues: 50
  loop : -0.96 (0.52), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 189 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.018   0.002   PHE A 176 
 TRP   0.016   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4123)
  covalent geometry    : angle       0.63541 ( 5595)
  SS BOND              : bond        0.00507 (    1)
  SS BOND              : angle       0.90253 (    2)
  hydrogen bonds       : bond        0.04261 (  283)
  hydrogen bonds       : angle       4.96489 (  822)

*********************** 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
  155 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   22 ILE cc_start: 0.8317 (mp) cc_final: 0.7945 (mm)
REVERT: A  127 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7401 (mm-30)
REVERT: A  146 ASN cc_start: 0.8690 (m-40) cc_final: 0.8295 (m110)
REVERT: A  167 CYS cc_start: 0.7941 (m) cc_final: 0.7442 (p)
REVERT: A  176 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8413 (t80)
REVERT: A  178 PHE cc_start: 0.7282 (t80) cc_final: 0.7005 (t80)
REVERT: A  186 LEU cc_start: 0.8369 (mm) cc_final: 0.8128 (mm)
REVERT: A  354 LYS cc_start: 0.8043 (tttm) cc_final: 0.7805 (tttp)
REVERT: A  426 ASP cc_start: 0.8450 (t70) cc_final: 0.8010 (t70)
REVERT: A  430 CYS cc_start: 0.7272 (t) cc_final: 0.6815 (t)
REVERT: A  462 LEU cc_start: 0.8417 (mm) cc_final: 0.8104 (mm)
REVERT: D   77 ASP cc_start: 0.7507 (m-30) cc_final: 0.7128 (m-30)
REVERT: D  114 TRP cc_start: 0.7599 (m-10) cc_final: 0.6971 (m-10)
  outliers start: 11
  outliers final: 8
  residues processed: 148
  average time/residue: 0.0601
  time to fit residues: 11.0784
Evaluate side-chains
  144 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
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  452 LEU
Chi-restraints excluded: chain D residue   29 VAL
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 44 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 329 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.182342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.142663 restraints weight = 6916.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.146866 restraints weight = 3805.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.149565 restraints weight = 2491.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.151200 restraints weight = 1856.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.152448 restraints weight = 1531.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4124  Z= 0.134
  Angle     :  0.639   8.018   5597  Z= 0.318
  Chirality :  0.043   0.171    650
  Planarity :  0.004   0.043    702
  Dihedral  :  4.220  13.538    570
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.99 %
    Favored  : 74.07 %
  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:  1.21 (0.38), residues: 524
  helix:  1.64 (0.28), residues: 344
  sheet: -0.39 (0.79), residues: 50
  loop : -0.90 (0.53), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 413 
 TYR   0.020   0.001   TYR A 182 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.019   0.001   TRP A 328 
 HIS   0.003   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4123)
  covalent geometry    : angle       0.63856 ( 5595)
  SS BOND              : bond        0.00447 (    1)
  SS BOND              : angle       0.67850 (    2)
  hydrogen bonds       : bond        0.04019 (  283)
  hydrogen bonds       : angle       4.89129 (  822)

*********************** 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
  160 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8270 (mp) cc_final: 0.7930 (mm)
REVERT: A  127 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7480 (mm-30)
REVERT: A  134 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7988 (mm)
REVERT: A  176 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8373 (t80)
REVERT: A  186 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8128 (mm)
REVERT: A  354 LYS cc_start: 0.8037 (tttm) cc_final: 0.7785 (tttp)
REVERT: A  462 LEU cc_start: 0.8406 (mm) cc_final: 0.8078 (mm)
REVERT: D   77 ASP cc_start: 0.7493 (m-30) cc_final: 0.7124 (m-30)
REVERT: D  114 TRP cc_start: 0.7595 (m-10) cc_final: 0.6947 (m-10)
  outliers start: 17
  outliers final: 9
  residues processed: 148
  average time/residue: 0.0589
  time to fit residues: 10.7795
Evaluate side-chains
  145 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  262 ASP
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   29 VAL
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 51 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.181925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.142896 restraints weight = 6976.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.147096 restraints weight = 3808.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.149824 restraints weight = 2480.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.151564 restraints weight = 1830.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.152802 restraints weight = 1488.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4124  Z= 0.134
  Angle     :  0.641   7.107   5597  Z= 0.318
  Chirality :  0.043   0.177    650
  Planarity :  0.005   0.055    702
  Dihedral  :  4.225  17.725    570
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.38 %
    Favored  : 73.15 %
  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:  1.26 (0.38), residues: 524
  helix:  1.70 (0.28), residues: 343
  sheet: -0.28 (0.80), residues: 50
  loop : -0.98 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 413 
 TYR   0.017   0.001   TYR A 182 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.028   0.002   TRP A 328 
 HIS   0.002   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4123)
  covalent geometry    : angle       0.64089 ( 5595)
  SS BOND              : bond        0.00359 (    1)
  SS BOND              : angle       0.63504 (    2)
  hydrogen bonds       : bond        0.03916 (  283)
  hydrogen bonds       : angle       4.84952 (  822)

*********************** 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
  153 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8251 (mp) cc_final: 0.7936 (mm)
REVERT: A  127 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: A  134 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: A  186 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8171 (mm)
REVERT: A  305 ASN cc_start: 0.8488 (m-40) cc_final: 0.8199 (m110)
REVERT: A  354 LYS cc_start: 0.8019 (tttm) cc_final: 0.7757 (tttp)
REVERT: A  426 ASP cc_start: 0.8537 (t70) cc_final: 0.7826 (t70)
REVERT: A  462 LEU cc_start: 0.8390 (mm) cc_final: 0.8081 (mm)
REVERT: D   77 ASP cc_start: 0.7471 (m-30) cc_final: 0.7057 (m-30)
REVERT: D  114 TRP cc_start: 0.7678 (m-10) cc_final: 0.6997 (m-10)
  outliers start: 15
  outliers final: 9
  residues processed: 143
  average time/residue: 0.0544
  time to fit residues: 9.7534
Evaluate side-chains
  146 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0670
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:   20.0000
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.184079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.145160 restraints weight = 7058.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.149310 restraints weight = 3878.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.152082 restraints weight = 2533.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.153901 restraints weight = 1867.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154998 restraints weight = 1514.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4124  Z= 0.128
  Angle     :  0.645   7.871   5597  Z= 0.318
  Chirality :  0.044   0.188    650
  Planarity :  0.004   0.034    702
  Dihedral  :  4.183  14.248    570
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.00 %
    Favored  : 71.53 %
  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:  1.27 (0.38), residues: 524
  helix:  1.65 (0.28), residues: 344
  sheet: -0.19 (0.82), residues: 50
  loop : -0.85 (0.54), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 413 
 TYR   0.015   0.001   TYR A 182 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.027   0.002   TRP A 328 
 HIS   0.002   0.000   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4123)
  covalent geometry    : angle       0.64501 ( 5595)
  SS BOND              : bond        0.00316 (    1)
  SS BOND              : angle       0.57813 (    2)
  hydrogen bonds       : bond        0.03781 (  283)
  hydrogen bonds       : angle       4.78622 (  822)

*********************** 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
  162 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8247 (mp) cc_final: 0.7966 (mm)
REVERT: A  127 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7494 (mm-30)
REVERT: A  134 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8063 (mm)
REVERT: A  186 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8188 (mm)
REVERT: A  305 ASN cc_start: 0.8470 (m-40) cc_final: 0.8157 (m110)
REVERT: A  354 LYS cc_start: 0.7999 (tttm) cc_final: 0.7734 (tttp)
REVERT: A  462 LEU cc_start: 0.8413 (mm) cc_final: 0.8135 (mm)
REVERT: D   77 ASP cc_start: 0.7458 (m-30) cc_final: 0.7042 (m-30)
REVERT: D  114 TRP cc_start: 0.7675 (m-10) cc_final: 0.6973 (m-10)
  outliers start: 15
  outliers final: 8
  residues processed: 152
  average time/residue: 0.0629
  time to fit residues: 12.1406
Evaluate side-chains
  144 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  186 LEU
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   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 22 optimal weight:    0.8980
   chunk 48 optimal weight:    0.1980
   chunk 29 optimal weight:    0.0030
   chunk 30 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0470
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.2688

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.186848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.147458 restraints weight = 7132.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.151593 restraints weight = 3943.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.154364 restraints weight = 2598.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.156058 restraints weight = 1929.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.157388 restraints weight = 1581.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   4124  Z= 0.125
  Angle     :  0.634   7.487   5597  Z= 0.314
  Chirality :  0.043   0.175    650
  Planarity :  0.004   0.033    702
  Dihedral  :  4.116  13.955    570
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 26.16 %
    Favored  : 71.30 %
  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:  1.37 (0.38), residues: 524
  helix:  1.69 (0.28), residues: 343
  sheet:  0.04 (0.82), residues: 49
  loop : -0.77 (0.54), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  65 
 TYR   0.015   0.001   TYR A 182 
 PHE   0.015   0.001   PHE A 348 
 TRP   0.034   0.002   TRP A 328 
 HIS   0.002   0.000   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4123)
  covalent geometry    : angle       0.63353 ( 5595)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       0.56667 (    2)
  hydrogen bonds       : bond        0.03658 (  283)
  hydrogen bonds       : angle       4.78181 (  822)

*********************** 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
  160 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7634 (mm-30)
REVERT: A  186 LEU cc_start: 0.8399 (mm) cc_final: 0.8114 (mm)
REVERT: A  230 MET cc_start: 0.8795 (tmm) cc_final: 0.8578 (tmm)
REVERT: A  305 ASN cc_start: 0.8402 (m-40) cc_final: 0.8115 (m110)
REVERT: A  354 LYS cc_start: 0.7956 (tttm) cc_final: 0.7690 (tttp)
REVERT: A  397 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7069 (ttm)
REVERT: D   77 ASP cc_start: 0.7416 (m-30) cc_final: 0.6981 (m-30)
REVERT: D  114 TRP cc_start: 0.7625 (m-10) cc_final: 0.6918 (m-10)
  outliers start: 11
  outliers final: 7
  residues processed: 153
  average time/residue: 0.0560
  time to fit residues: 10.9076
Evaluate side-chains
  149 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
A 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.184445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.144836 restraints weight = 7018.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.149002 restraints weight = 3886.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.151710 restraints weight = 2562.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.153574 restraints weight = 1909.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.154762 restraints weight = 1555.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4124  Z= 0.138
  Angle     :  0.693  11.039   5597  Z= 0.335
  Chirality :  0.044   0.226    650
  Planarity :  0.005   0.074    702
  Dihedral  :  4.122  13.316    570
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 26.16 %
    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 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:  1.29 (0.38), residues: 524
  helix:  1.65 (0.28), residues: 343
  sheet: -0.11 (0.82), residues: 50
  loop : -0.79 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 413 
 TYR   0.023   0.002   TYR A 182 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.037   0.002   TRP A 328 
 HIS   0.001   0.000   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4123)
  covalent geometry    : angle       0.69267 ( 5595)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       0.54785 (    2)
  hydrogen bonds       : bond        0.03797 (  283)
  hydrogen bonds       : angle       4.71427 (  822)

*********************** 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
  159 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   16 ARG cc_start: 0.6278 (tpp-160) cc_final: 0.5588 (ptt180)
REVERT: A  127 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7620 (mm-30)
REVERT: A  134 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8082 (mm)
REVERT: A  186 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: A  354 LYS cc_start: 0.7977 (tttm) cc_final: 0.7706 (tttp)
REVERT: A  374 CYS cc_start: 0.7303 (m) cc_final: 0.6970 (m)
REVERT: D   77 ASP cc_start: 0.7418 (m-30) cc_final: 0.7006 (m-30)
REVERT: D  114 TRP cc_start: 0.7672 (m-10) cc_final: 0.6953 (m-10)
  outliers start: 15
  outliers final: 9
  residues processed: 150
  average time/residue: 0.0498
  time to fit residues: 9.4323
Evaluate side-chains
  148 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  375 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0170
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0030
   chunk 25 optimal weight:    0.4980
   chunk 41 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.3828

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4203 r_free = 0.4203 target = 0.184591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.145728 restraints weight = 7118.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.149960 restraints weight = 3867.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.152709 restraints weight = 2509.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.154405 restraints weight = 1850.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.155550 restraints weight = 1510.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4124  Z= 0.127
  Angle     :  0.685   8.261   5597  Z= 0.331
  Chirality :  0.046   0.245    650
  Planarity :  0.005   0.077    702
  Dihedral  :  4.158  16.939    570
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 27.08 %
    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 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:  1.26 (0.38), residues: 524
  helix:  1.64 (0.28), residues: 341
  sheet:  0.11 (0.82), residues: 49
  loop : -0.92 (0.54), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.022   0.001   TYR A 182 
 PHE   0.015   0.001   PHE A 348 
 TRP   0.039   0.002   TRP A 328 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4123)
  covalent geometry    : angle       0.68502 ( 5595)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       0.56447 (    2)
  hydrogen bonds       : bond        0.03667 (  283)
  hydrogen bonds       : angle       4.74192 (  822)

*********************** 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
  157 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6047 (tpp-160) cc_final: 0.5015 (ptp-170)
REVERT: A  127 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: A  186 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8145 (mm)
REVERT: A  192 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7564 (tm-30)
REVERT: A  230 MET cc_start: 0.8760 (tmm) cc_final: 0.8530 (tmm)
REVERT: A  354 LYS cc_start: 0.7971 (tttm) cc_final: 0.7705 (tttp)
REVERT: A  374 CYS cc_start: 0.7247 (m) cc_final: 0.6977 (m)
REVERT: A  397 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7105 (ttm)
REVERT: A  426 ASP cc_start: 0.8502 (t70) cc_final: 0.7800 (t70)
REVERT: D   65 ARG cc_start: 0.6867 (ptm160) cc_final: 0.6422 (ptt-90)
REVERT: D   77 ASP cc_start: 0.7460 (m-30) cc_final: 0.7079 (m-30)
REVERT: D  114 TRP cc_start: 0.7662 (m-10) cc_final: 0.6938 (m-10)
  outliers start: 15
  outliers final: 9
  residues processed: 148
  average time/residue: 0.0520
  time to fit residues: 9.8212
Evaluate side-chains
  151 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  375 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.184133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.145022 restraints weight = 7034.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.149183 restraints weight = 3880.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.151910 restraints weight = 2536.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.153720 restraints weight = 1881.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.154818 restraints weight = 1533.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4124  Z= 0.142
  Angle     :  0.707  11.310   5597  Z= 0.341
  Chirality :  0.045   0.228    650
  Planarity :  0.005   0.071    702
  Dihedral  :  4.094  13.252    570
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 28.01 %
    Favored  : 69.21 %
  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:  1.28 (0.38), residues: 524
  helix:  1.66 (0.28), residues: 342
  sheet: -0.05 (0.82), residues: 50
  loop : -0.87 (0.56), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  65 
 TYR   0.023   0.002   TYR A 243 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.042   0.003   TRP A 328 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4123)
  covalent geometry    : angle       0.70748 ( 5595)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       0.55406 (    2)
  hydrogen bonds       : bond        0.03821 (  283)
  hydrogen bonds       : angle       4.75075 (  822)

********************** 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
  152 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   16 ARG cc_start: 0.6063 (tpp-160) cc_final: 0.5027 (ptp-170)
REVERT: A  127 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7712 (mm-30)
REVERT: A  186 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (mm)
REVERT: A  192 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7271 (tm-30)
REVERT: A  354 LYS cc_start: 0.7936 (tttm) cc_final: 0.7658 (tttp)
REVERT: A  374 CYS cc_start: 0.7139 (m) cc_final: 0.6924 (m)
REVERT: A  426 ASP cc_start: 0.8729 (t70) cc_final: 0.8047 (t70)
REVERT: D   65 ARG cc_start: 0.6898 (ptm160) cc_final: 0.6437 (ptt-90)
REVERT: D   77 ASP cc_start: 0.7478 (m-30) cc_final: 0.7091 (m-30)
REVERT: D  114 TRP cc_start: 0.7709 (m-10) cc_final: 0.6966 (m-10)
  outliers start: 12
  outliers final: 10
  residues processed: 145
  average time/residue: 0.0593
  time to fit residues: 11.0387
Evaluate side-chains
  150 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  375 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0470
   overall best weight:    0.3478

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.186689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.146357 restraints weight = 7075.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.150480 restraints weight = 3914.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.153285 restraints weight = 2590.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.155122 restraints weight = 1935.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.156398 restraints weight = 1580.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4124  Z= 0.131
  Angle     :  0.702  10.255   5597  Z= 0.339
  Chirality :  0.045   0.220    650
  Planarity :  0.005   0.063    702
  Dihedral  :  4.057  13.486    570
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 27.31 %
    Favored  : 69.21 %
  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:  1.29 (0.38), residues: 524
  helix:  1.65 (0.28), residues: 341
  sheet:  0.16 (0.82), residues: 49
  loop : -0.86 (0.55), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 189 
 TYR   0.028   0.002   TYR A 243 
 PHE   0.016   0.001   PHE A 348 
 TRP   0.041   0.003   TRP A 328 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4123)
  covalent geometry    : angle       0.70190 ( 5595)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.56338 (    2)
  hydrogen bonds       : bond        0.03761 (  283)
  hydrogen bonds       : angle       4.74509 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 908.47 seconds
wall clock time: 16 minutes 15.10 seconds (975.10 seconds total)