Starting phenix.real_space_refine
on Sat Apr  4 20:06:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u4j_63848/04_2026/9u4j_63848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u4j_63848/04_2026/9u4j_63848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u4j_63848/04_2026/9u4j_63848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u4j_63848/04_2026/9u4j_63848.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u4j_63848/04_2026/9u4j_63848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u4j_63848/04_2026/9u4j_63848.cif"
  }
  resolution = 3.4
  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=  -0.044 sd=   0.182
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       5      5.16       5
     C    1266      2.51       5
     N     333      2.21       5
     O     333      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1937
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 1937
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 11, 'TRANS': 261}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 296
          Unresolved non-hydrogen angles: 378
          Unresolved non-hydrogen dihedrals: 256
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 184
  Time building chain proxies: 0.43, per 1000 atoms: 0.22
  Number of scatterers: 1937
  At special positions: 0
  Unit cell: (61.42, 63.64, 76.96, 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       5     16.00
     O     333      8.00
     N     333      7.00
     C    1266      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.09
  Conformation dependent library (CDL) restraints added in 101.3 milliseconds
  

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  518

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      83.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 46
      removed outlier: 3.919A  pdb=" N   VAL A  30 " --> pdb=" O   PHE A  26 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LEU A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      Proline residue:  A  33  - end of helix
      removed outlier: 3.790A  pdb=" N   ARG A  44 " --> pdb=" O   TRP A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 49
      No H-bonds generated for 'chain 'A' and resid 47 through 49'
    Processing helix  chain 'A' and resid 52 through 69
    Processing helix  chain 'A' and resid 71 through 76
    Processing helix  chain 'A' and resid 86 through 120
      removed outlier: 4.077A  pdb=" N   CYS A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LYS A  91 " --> pdb=" O   PRO A  87 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE A  95 " --> pdb=" O   LYS A  91 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   ILE A  96 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN A 100 " --> pdb=" O   ILE A  96 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   ILE A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA A 106 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 133
    Processing helix  chain 'A' and resid 135 through 151
    Processing helix  chain 'A' and resid 152 through 158
      removed outlier: 5.297A  pdb=" N   HIS A 155 " --> pdb=" O   PRO A 152 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ASP A 156 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU A 157 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU A 158 " --> pdb=" O   HIS A 155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 152 through 158'
    Processing helix  chain 'A' and resid 175 through 190
      removed outlier: 3.526A  pdb=" N   PHE A 190 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 212
    Processing helix  chain 'A' and resid 216 through 254
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 260 through 265
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 274 through 276
      No H-bonds generated for 'chain 'A' and resid 274 through 276'
    Processing helix  chain 'A' and resid 277 through 285
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.710A  pdb=" N   VAL A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 290'

    141 hydrogen bonds defined for protein.
    417 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: 0.17

  Time building geometry restraints manager: 0.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 619
        1.34 -     1.46: 303
        1.46 -     1.57: 1059
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 1987
  Sorted by residual:
  bond pdb=" CB  ASP A 114 "
       pdb=" CG  ASP A 114 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.82e+00
  bond pdb=" CB  GLN A  48 "
       pdb=" CG  GLN A  48 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.16e+00
  bond pdb=" CA  ASP A 114 "
       pdb=" CB  ASP A 114 "
    ideal  model  delta    sigma   weight residual
    1.528  1.543 -0.015 1.56e-02 4.11e+03 9.03e-01
  bond pdb=" C   TYR A  98 "
       pdb=" O   TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.29e-02 6.01e+03 7.70e-01
  bond pdb=" N   ILE A 103 "
       pdb=" CA  ILE A 103 "
    ideal  model  delta    sigma   weight residual
    1.452  1.462 -0.010 1.18e-02 7.18e+03 6.98e-01
  ... (remaining 1982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 2632
        1.72 -     3.43: 71
        3.43 -     5.15: 18
        5.15 -     6.86: 2
        6.86 -     8.58: 4
  Bond angle restraints: 2727
  Sorted by residual:
  angle pdb=" CA  GLN A  48 "
        pdb=" CB  GLN A  48 "
        pdb=" CG  GLN A  48 "
      ideal   model   delta    sigma   weight residual
     114.10  121.18   -7.08 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" N   ASN A 290 "
        pdb=" CA  ASN A 290 "
        pdb=" C   ASN A 290 "
      ideal   model   delta    sigma   weight residual
     109.40  114.20   -4.80 1.63e+00 3.76e-01 8.68e+00
  angle pdb=" N   PHE A 187 "
        pdb=" CA  PHE A 187 "
        pdb=" C   PHE A 187 "
      ideal   model   delta    sigma   weight residual
     111.36  114.42   -3.06 1.09e+00 8.42e-01 7.89e+00
  angle pdb=" CA  PRO A  33 "
        pdb=" N   PRO A  33 "
        pdb=" CD  PRO A  33 "
      ideal   model   delta    sigma   weight residual
     112.00  108.31    3.69 1.40e+00 5.10e-01 6.93e+00
  angle pdb=" CA  ASP A 114 "
        pdb=" CB  ASP A 114 "
        pdb=" CG  ASP A 114 "
      ideal   model   delta    sigma   weight residual
     112.60  115.22   -2.62 1.00e+00 1.00e+00 6.88e+00
  ... (remaining 2722 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 1010
       17.05 -    34.10: 94
       34.10 -    51.14: 28
       51.14 -    68.19: 3
       68.19 -    85.24: 2
  Dihedral angle restraints: 1137
    sinusoidal: 338
      harmonic: 799
  Sorted by residual:
  dihedral pdb=" CA  HIS A  80 "
           pdb=" C   HIS A  80 "
           pdb=" N   ASP A  81 "
           pdb=" CA  ASP A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.70   17.30     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ALA A 134 "
           pdb=" C   ALA A 134 "
           pdb=" N   VAL A 135 "
           pdb=" CA  VAL A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.03   16.97     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  ALA A 267 "
           pdb=" C   ALA A 267 "
           pdb=" N   TYR A 268 "
           pdb=" CA  TYR A 268 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.37   16.63     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 199
       0.034 -    0.069: 84
       0.069 -    0.103: 28
       0.103 -    0.137: 7
       0.137 -    0.171: 4
  Chirality restraints: 322
  Sorted by residual:
  chirality pdb=" CA  PRO A  33 "
            pdb=" N   PRO A  33 "
            pdb=" C   PRO A  33 "
            pdb=" CB  PRO A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.29e-01
  chirality pdb=" CB  VAL A 188 "
            pdb=" CA  VAL A 188 "
            pdb=" CG1 VAL A 188 "
            pdb=" CG2 VAL A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.92e-01
  chirality pdb=" CB  ILE A 103 "
            pdb=" CA  ILE A 103 "
            pdb=" CG1 ILE A 103 "
            pdb=" CG2 ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.28e-01
  ... (remaining 319 not shown)

  Planarity restraints: 347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 238 "   -0.048 5.00e-02 4.00e+02   7.21e-02 8.31e+00
        pdb=" N   PRO A 239 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 239 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 239 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  32 "   -0.048 5.00e-02 4.00e+02   7.18e-02 8.24e+00
        pdb=" N   PRO A  33 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A  33 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A  33 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 151 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO A 152 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 152 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 152 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 344 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 389
        2.76 -     3.30: 2083
        3.30 -     3.83: 3111
        3.83 -     4.37: 3213
        4.37 -     4.90: 5398
  Nonbonded interactions: 14194
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 165 "
            pdb=" ND1 HIS A 165 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" O   MET A  57 "
            pdb=" OG  SER A  60 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   HIS A  79 "
            pdb=" ND1 HIS A  79 "
     model   vdw
     2.442 3.120
  nonbonded pdb=" ND2 ASN A  35 "
            pdb=" O   SER A  60 "
     model   vdw
     2.498 3.120
  nonbonded pdb=" O   ARG A 160 "
            pdb=" NH1 ARG A 160 "
     model   vdw
     2.504 3.120
  ... (remaining 14189 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             2.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.040
  Find NCS groups from input model:        0.000
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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      :  0.004   0.041   1987  Z= 0.182
  Angle     :  0.761   8.578   2727  Z= 0.411
  Chirality :  0.044   0.171    322
  Planarity :  0.007   0.072    347
  Dihedral  : 15.658  85.236    619
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.72 %
    Favored  : 84.05 %
  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 are not related in a simple way.
  whole: -0.11 (0.54), residues: 267
  helix:  1.30 (0.39), residues: 184
  sheet:  None (None), residues: 0
  loop : -3.42 (0.67), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 224 
 TYR   0.017   0.002   TYR A  55 
 PHE   0.011   0.001   PHE A 274 
 TRP   0.014   0.002   TRP A 194 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 1987)
  covalent geometry    : angle       0.76117 ( 2727)
  hydrogen bonds       : bond        0.10752 (  141)
  hydrogen bonds       : angle       5.18513 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  114 ASP cc_start: 0.8115 (t0) cc_final: 0.7865 (t0)
REVERT: A  282 ASP cc_start: 0.8530 (m-30) cc_final: 0.8236 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0627
  time to fit residues: 3.6899
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0670
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.2096

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.074656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.068919 restraints weight = 9423.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.00
r_work: 0.3304 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   1987  Z= 0.127
  Angle     :  0.634   6.658   2727  Z= 0.326
  Chirality :  0.041   0.138    322
  Planarity :  0.006   0.060    347
  Dihedral  :  4.492  17.947    290
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.50 %
    Favored  : 84.66 %
  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 are not related in a simple way.
  whole:  0.59 (0.56), residues: 267
  helix:  1.46 (0.38), residues: 190
  sheet:  None (None), residues: 0
  loop : -2.46 (0.82), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  49 
 TYR   0.007   0.001   TYR A  55 
 PHE   0.010   0.001   PHE A  97 
 TRP   0.005   0.001   TRP A  73 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 1987)
  covalent geometry    : angle       0.63437 ( 2727)
  hydrogen bonds       : bond        0.03323 (  141)
  hydrogen bonds       : angle       4.13250 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.076 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 54
  average time/residue: 0.0640
  time to fit residues: 3.9787
Evaluate side-chains
  50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0470
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.072033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.066128 restraints weight = 9405.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.89
r_work: 0.3231 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   1987  Z= 0.159
  Angle     :  0.671   6.160   2727  Z= 0.356
  Chirality :  0.043   0.162    322
  Planarity :  0.006   0.054    347
  Dihedral  :  4.708  17.068    290
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 21.47 %
    Favored  : 77.30 %
  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 are not related in a simple way.
  whole:  0.13 (0.54), residues: 267
  helix:  1.35 (0.37), residues: 188
  sheet:  None (None), residues: 0
  loop : -3.19 (0.74), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  49 
 TYR   0.008   0.001   TYR A  66 
 PHE   0.018   0.002   PHE A 190 
 TRP   0.016   0.002   TRP A  73 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 1987)
  covalent geometry    : angle       0.67072 ( 2727)
  hydrogen bonds       : bond        0.04553 (  141)
  hydrogen bonds       : angle       4.48473 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A   66 TYR cc_start: 0.8562 (t80) cc_final: 0.8335 (t80)
REVERT: A  102 TYR cc_start: 0.8352 (m-10) cc_final: 0.7939 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 47
  average time/residue: 0.0754
  time to fit residues: 4.0349
Evaluate side-chains
  46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  230 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.071320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.065473 restraints weight = 9426.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.86
r_work: 0.3220 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   1987  Z= 0.169
  Angle     :  0.678   5.738   2727  Z= 0.359
  Chirality :  0.044   0.190    322
  Planarity :  0.006   0.060    347
  Dihedral  :  4.813  18.960    290
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 22.09 %
    Favored  : 76.07 %
  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 are not related in a simple way.
  whole: -0.00 (0.53), residues: 267
  helix:  1.33 (0.38), residues: 183
  sheet:  None (None), residues: 0
  loop : -3.18 (0.67), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 224 
 TYR   0.010   0.002   TYR A  55 
 PHE   0.012   0.001   PHE A 274 
 TRP   0.018   0.002   TRP A  73 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 1987)
  covalent geometry    : angle       0.67775 ( 2727)
  hydrogen bonds       : bond        0.04601 (  141)
  hydrogen bonds       : angle       4.49361 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   66 TYR cc_start: 0.8604 (t80) cc_final: 0.8403 (t80)
REVERT: A  102 TYR cc_start: 0.8385 (m-10) cc_final: 0.7879 (m-80)
REVERT: A  269 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.6366 (t-170)
REVERT: A  282 ASP cc_start: 0.8496 (m-30) cc_final: 0.8239 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0646
  time to fit residues: 3.4521
Evaluate side-chains
  48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  269 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.069273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.063385 restraints weight = 9452.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.82
r_work: 0.3161 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   1987  Z= 0.231
  Angle     :  0.741   5.935   2727  Z= 0.401
  Chirality :  0.048   0.217    322
  Planarity :  0.007   0.065    347
  Dihedral  :  5.229  20.079    290
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.09 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.52), residues: 267
  helix:  1.01 (0.38), residues: 182
  sheet:  None (None), residues: 0
  loop : -3.53 (0.64), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 160 
 TYR   0.010   0.002   TYR A  43 
 PHE   0.020   0.002   PHE A 190 
 TRP   0.025   0.003   TRP A  73 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 1987)
  covalent geometry    : angle       0.74086 ( 2727)
  hydrogen bonds       : bond        0.05710 (  141)
  hydrogen bonds       : angle       4.87389 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A  102 TYR cc_start: 0.8461 (m-10) cc_final: 0.8066 (m-80)
REVERT: A  269 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.6432 (t-170)
REVERT: A  282 ASP cc_start: 0.8535 (m-30) cc_final: 0.8283 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 0.0644
  time to fit residues: 3.5938
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  289 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0050
   chunk 14 optimal weight:    0.0170
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.3632

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.071919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.066097 restraints weight = 9327.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.83
r_work: 0.3227 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1987  Z= 0.147
  Angle     :  0.661   5.574   2727  Z= 0.349
  Chirality :  0.044   0.184    322
  Planarity :  0.007   0.074    347
  Dihedral  :  4.804  20.210    290
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 25.15 %
    Favored  : 73.01 %
  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 are not related in a simple way.
  whole:  0.06 (0.53), residues: 267
  helix:  1.37 (0.38), residues: 180
  sheet:  None (None), residues: 0
  loop : -2.99 (0.67), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 160 
 TYR   0.012   0.001   TYR A 201 
 PHE   0.008   0.001   PHE A 274 
 TRP   0.016   0.001   TRP A  73 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 1987)
  covalent geometry    : angle       0.66091 ( 2727)
  hydrogen bonds       : bond        0.04070 (  141)
  hydrogen bonds       : angle       4.43854 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.043 
Fit side-chains
REVERT: A  102 TYR cc_start: 0.8344 (m-10) cc_final: 0.8031 (m-80)
REVERT: A  282 ASP cc_start: 0.8537 (m-30) cc_final: 0.8274 (m-30)
  outliers start: 3
  outliers final: 3
  residues processed: 48
  average time/residue: 0.0599
  time to fit residues: 3.2810
Evaluate side-chains
  48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  289 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.069915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.064026 restraints weight = 9417.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.80
r_work: 0.3176 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1987  Z= 0.194
  Angle     :  0.710   5.860   2727  Z= 0.380
  Chirality :  0.046   0.231    322
  Planarity :  0.007   0.077    347
  Dihedral  :  5.031  20.778    290
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 27.61 %
    Favored  : 69.33 %
  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 are not related in a simple way.
  whole: -0.16 (0.52), residues: 267
  helix:  1.20 (0.38), residues: 180
  sheet:  None (None), residues: 0
  loop : -3.07 (0.64), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 224 
 TYR   0.011   0.001   TYR A  66 
 PHE   0.013   0.001   PHE A 274 
 TRP   0.009   0.001   TRP A 194 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 1987)
  covalent geometry    : angle       0.71032 ( 2727)
  hydrogen bonds       : bond        0.05141 (  141)
  hydrogen bonds       : angle       4.70859 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.042 
Fit side-chains
REVERT: A  102 TYR cc_start: 0.8417 (m-10) cc_final: 0.8030 (m-80)
REVERT: A  269 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.6609 (t-170)
REVERT: A  282 ASP cc_start: 0.8536 (m-30) cc_final: 0.8282 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0542
  time to fit residues: 2.9069
Evaluate side-chains
  48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  289 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0030
   chunk 19 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0570
   overall best weight:    0.3308

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.072326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.066340 restraints weight = 9694.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.01
r_work: 0.3233 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1987  Z= 0.141
  Angle     :  0.672   6.197   2727  Z= 0.349
  Chirality :  0.044   0.200    322
  Planarity :  0.006   0.075    347
  Dihedral  :  4.691  20.568    290
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 28.22 %
    Favored  : 68.71 %
  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 are not related in a simple way.
  whole:  0.26 (0.53), residues: 267
  helix:  1.46 (0.38), residues: 180
  sheet:  None (None), residues: 0
  loop : -2.75 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 224 
 TYR   0.010   0.001   TYR A 201 
 PHE   0.007   0.001   PHE A 274 
 TRP   0.005   0.001   TRP A 142 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 1987)
  covalent geometry    : angle       0.67155 ( 2727)
  hydrogen bonds       : bond        0.03839 (  141)
  hydrogen bonds       : angle       4.35419 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  102 TYR cc_start: 0.8360 (m-10) cc_final: 0.8041 (m-80)
REVERT: A  269 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.6670 (t-170)
REVERT: A  282 ASP cc_start: 0.8546 (m-30) cc_final: 0.8288 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0594
  time to fit residues: 3.1952
Evaluate side-chains
  46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  269 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.070918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.065019 restraints weight = 9365.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.86
r_work: 0.3206 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   1987  Z= 0.176
  Angle     :  0.767  15.396   2727  Z= 0.380
  Chirality :  0.045   0.234    322
  Planarity :  0.007   0.097    347
  Dihedral  :  4.944  25.537    290
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 27.61 %
    Favored  : 69.33 %
  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 are not related in a simple way.
  whole:  0.06 (0.52), residues: 267
  helix:  1.35 (0.38), residues: 180
  sheet:  None (None), residues: 0
  loop : -2.94 (0.65), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 224 
 TYR   0.008   0.001   TYR A  55 
 PHE   0.011   0.001   PHE A 274 
 TRP   0.008   0.001   TRP A 194 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 1987)
  covalent geometry    : angle       0.76675 ( 2727)
  hydrogen bonds       : bond        0.04715 (  141)
  hydrogen bonds       : angle       4.49899 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  102 TYR cc_start: 0.8398 (m-10) cc_final: 0.8089 (m-80)
REVERT: A  269 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.6679 (t-170)
REVERT: A  282 ASP cc_start: 0.8542 (m-30) cc_final: 0.8279 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0653
  time to fit residues: 3.5394
Evaluate side-chains
  46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  289 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0980
   chunk 10 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.3980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.072049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.066013 restraints weight = 9574.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 3.00
r_work: 0.3226 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1987  Z= 0.152
  Angle     :  0.749  13.575   2727  Z= 0.371
  Chirality :  0.044   0.223    322
  Planarity :  0.007   0.098    347
  Dihedral  :  4.829  26.438    290
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 28.22 %
    Favored  : 68.71 %
  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 are not related in a simple way.
  whole:  0.22 (0.53), residues: 267
  helix:  1.39 (0.38), residues: 181
  sheet:  None (None), residues: 0
  loop : -2.69 (0.68), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 224 
 TYR   0.009   0.001   TYR A 201 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.006   0.001   TRP A 194 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 1987)
  covalent geometry    : angle       0.74948 ( 2727)
  hydrogen bonds       : bond        0.04063 (  141)
  hydrogen bonds       : angle       4.37471 (  417)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  102 TYR cc_start: 0.8378 (m-10) cc_final: 0.8080 (m-80)
REVERT: A  269 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.6759 (t-170)
REVERT: A  282 ASP cc_start: 0.8558 (m-30) cc_final: 0.8300 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 48
  average time/residue: 0.0580
  time to fit residues: 3.1760
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  289 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 17 optimal weight:    0.2980
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.071504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.065257 restraints weight = 9818.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 3.04
r_work: 0.3198 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1987  Z= 0.171
  Angle     :  0.769  13.749   2727  Z= 0.384
  Chirality :  0.045   0.233    322
  Planarity :  0.007   0.100    347
  Dihedral  :  4.930  27.269    290
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 27.61 %
    Favored  : 68.71 %
  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 are not related in a simple way.
  whole:  0.01 (0.52), residues: 267
  helix:  1.28 (0.38), residues: 181
  sheet:  None (None), residues: 0
  loop : -2.94 (0.63), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 263 
 TYR   0.017   0.002   TYR A  55 
 PHE   0.010   0.001   PHE A 274 
 TRP   0.008   0.001   TRP A 194 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 1987)
  covalent geometry    : angle       0.76940 ( 2727)
  hydrogen bonds       : bond        0.04535 (  141)
  hydrogen bonds       : angle       4.49863 (  417)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 705.57 seconds
wall clock time: 13 minutes 40.07 seconds (820.07 seconds total)