Starting phenix.real_space_refine
on Wed Sep 17 03:06:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6yv1_10940/09_2025/6yv1_10940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6yv1_10940/09_2025/6yv1_10940.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6yv1_10940/09_2025/6yv1_10940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6yv1_10940/09_2025/6yv1_10940.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6yv1_10940/09_2025/6yv1_10940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6yv1_10940/09_2025/6yv1_10940.map"
  }
  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=   0.000 sd=   0.001
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      14      5.16       5
     C    1697      2.51       5
     N     363      2.21       5
     O     422      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2496
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2496
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 18, 'TRANS': 309}
          Chain breaks: 7
  Time building chain proxies: 0.91, per 1000 atoms: 0.36
  Number of scatterers: 2496
  At special positions: 0
  Unit cell: (56.079, 61.938, 73.656, 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      14     16.00
     O     422      8.00
     N     363      7.00
     C    1697      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: 0.20
  Conformation dependent library (CDL) restraints added in 97.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  612

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      76.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 42
    Processing helix  chain 'A' and resid 50 through 60
      removed outlier: 4.267A  pdb=" N   SER A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   SER A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASN A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 87
      removed outlier: 3.567A  pdb=" N   GLU A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 116
    Processing helix  chain 'A' and resid 120 through 137
      removed outlier: 3.564A  pdb=" N   CYS A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   CYS A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 167
    Processing helix  chain 'A' and resid 179 through 197
      removed outlier: 3.715A  pdb=" N   ILE A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 188 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 3.918A  pdb=" N   ALA A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   PHE A 225 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
      removed outlier: 3.805A  pdb=" N   THR A 242 " --> pdb=" O   ASN A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 258
      removed outlier: 3.638A  pdb=" N   ILE A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 276
      removed outlier: 3.727A  pdb=" N   SER A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 274 " --> pdb=" O   MET A 270 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   PHE A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 285
      removed outlier: 3.711A  pdb=" N   LEU A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLN A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 279 through 285'
    Processing helix  chain 'A' and resid 288 through 297
      removed outlier: 3.736A  pdb=" N   THR A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASP A 295 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 297 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 317
      removed outlier: 3.694A  pdb=" N   ALA A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLY A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 361
      removed outlier: 3.645A  pdb=" N   ILE A 361 " --> pdb=" O   PHE A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.519A  pdb=" N   ILE A 366 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 395
      removed outlier: 3.962A  pdb=" N   VAL A 375 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASN A 376 " --> pdb=" O   ASN A 372 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   TYR A 377 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE A 380 " --> pdb=" O   ASN A 376 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ALA A 381 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 427
      removed outlier: 3.678A  pdb=" N   LEU A 419 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 445

    142 hydrogen bonds defined for protein.
    420 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.35

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 520
        1.33 -     1.45: 554
        1.45 -     1.57: 1464
        1.57 -     1.69: 0
        1.69 -     1.81: 19
  Bond restraints: 2557
  Sorted by residual:
  bond pdb=" C   CYS A 144 "
       pdb=" O   CYS A 144 "
    ideal  model  delta    sigma   weight residual
    1.234  1.215  0.019 1.26e-02 6.30e+03 2.18e+00
  bond pdb=" C   LYS A 145 "
       pdb=" N   PRO A 146 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.18e-02 7.18e+03 1.47e+00
  bond pdb=" CA  PRO A 146 "
       pdb=" C   PRO A 146 "
    ideal  model  delta    sigma   weight residual
    1.517  1.527 -0.010 9.30e-03 1.16e+04 1.12e+00
  bond pdb=" C   PRO A 146 "
       pdb=" O   PRO A 146 "
    ideal  model  delta    sigma   weight residual
    1.240  1.229  0.011 1.12e-02 7.97e+03 1.00e+00
  bond pdb=" C   ILE A 444 "
       pdb=" O   ILE A 444 "
    ideal  model  delta    sigma   weight residual
    1.241  1.230  0.010 1.03e-02 9.43e+03 9.86e-01
  ... (remaining 2552 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 3376
        1.20 -     2.40: 87
        2.40 -     3.60: 19
        3.60 -     4.79: 5
        4.79 -     5.99: 13
  Bond angle restraints: 3500
  Sorted by residual:
  angle pdb=" C   ILE A 107 "
        pdb=" CA  ILE A 107 "
        pdb=" CB  ILE A 107 "
      ideal   model   delta    sigma   weight residual
     114.35  108.36    5.99 1.06e+00 8.90e-01 3.20e+01
  angle pdb=" N   VAL A  50 "
        pdb=" CA  VAL A  50 "
        pdb=" C   VAL A  50 "
      ideal   model   delta    sigma   weight residual
     113.53  108.73    4.80 9.80e-01 1.04e+00 2.40e+01
  angle pdb=" C   LYS A 145 "
        pdb=" N   PRO A 146 "
        pdb=" CA  PRO A 146 "
      ideal   model   delta    sigma   weight residual
     120.38  125.03   -4.65 1.03e+00 9.43e-01 2.04e+01
  angle pdb=" CA  ILE A 107 "
        pdb=" C   ILE A 107 "
        pdb=" N   PRO A 108 "
      ideal   model   delta    sigma   weight residual
     121.00  117.26    3.74 8.30e-01 1.45e+00 2.03e+01
  angle pdb=" N   GLY A 143 "
        pdb=" CA  GLY A 143 "
        pdb=" C   GLY A 143 "
      ideal   model   delta    sigma   weight residual
     112.73  118.02   -5.29 1.20e+00 6.94e-01 1.94e+01
  ... (remaining 3495 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.93: 1341
       15.93 -    31.87: 88
       31.87 -    47.80: 27
       47.80 -    63.73: 7
       63.73 -    79.67: 2
  Dihedral angle restraints: 1465
    sinusoidal: 515
      harmonic: 950
  Sorted by residual:
  dihedral pdb=" CA  LEU A 262 "
           pdb=" CB  LEU A 262 "
           pdb=" CG  LEU A 262 "
           pdb=" CD1 LEU A 262 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.91   59.09     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LEU A 298 "
           pdb=" CA  LEU A 298 "
           pdb=" CB  LEU A 298 "
           pdb=" CG  LEU A 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -9.24  -50.76     3      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CB  GLU A  85 "
           pdb=" CG  GLU A  85 "
           pdb=" CD  GLU A  85 "
           pdb=" OE1 GLU A  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.67   79.67     1      3.00e+01 1.11e-03 8.75e+00
  ... (remaining 1462 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 224
       0.022 -    0.043: 128
       0.043 -    0.065: 60
       0.065 -    0.087: 18
       0.087 -    0.109: 13
  Chirality restraints: 443
  Sorted by residual:
  chirality pdb=" CA  VAL A 142 "
            pdb=" N   VAL A 142 "
            pdb=" C   VAL A 142 "
            pdb=" CB  VAL A 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.33    0.11 2.00e-01 2.50e+01 2.95e-01
  chirality pdb=" CA  ILE A  44 "
            pdb=" N   ILE A  44 "
            pdb=" C   ILE A  44 "
            pdb=" CB  ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.83e-01
  chirality pdb=" CA  ILE A  90 "
            pdb=" N   ILE A  90 "
            pdb=" C   ILE A  90 "
            pdb=" CB  ILE A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.73e-01
  ... (remaining 440 not shown)

  Planarity restraints: 409
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 146 "    0.027 5.00e-02 4.00e+02   4.18e-02 2.80e+00
        pdb=" N   PRO A 147 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 147 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 147 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  63 "    0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A  64 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A  64 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  64 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 144 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.64e+00
        pdb=" C   CYS A 144 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   CYS A 144 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LYS A 145 "    0.007 2.00e-02 2.50e+03
  ... (remaining 406 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 730
        2.80 -     3.32: 2290
        3.32 -     3.85: 4012
        3.85 -     4.37: 4630
        4.37 -     4.90: 7978
  Nonbonded interactions: 19640
  Sorted by model distance:
  nonbonded pdb=" O   PHE A  49 "
            pdb=" OH  TYR A 135 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   LEU A 238 "
            pdb=" OG1 THR A 242 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   VAL A 309 "
            pdb=" OG1 THR A 313 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR A 226 "
            pdb=" O   LEU A 424 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OE1 GLU A 282 "
            pdb=" NH1 ARG A 296 "
     model   vdw
     2.417 3.120
  ... (remaining 19635 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:             2.930
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     4.740
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
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      :  0.002   0.022   2557  Z= 0.133
  Angle     :  0.580   5.992   3500  Z= 0.369
  Chirality :  0.036   0.109    443
  Planarity :  0.004   0.042    409
  Dihedral  : 12.662  79.667    853
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.89 %
    Favored  : 89.26 %
  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: -4.45 (0.37), residues: 312
  helix: -2.71 (0.26), residues: 228
  sheet:  None (None), residues: 0
  loop : -3.02 (0.62), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.006   0.001   TYR A 110 
 PHE   0.006   0.001   PHE A 311 
 TRP   0.004   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 2557)
  covalent geometry    : angle       0.58032 ( 3500)
  hydrogen bonds       : bond        0.25778 (  142)
  hydrogen bonds       : angle       7.72391 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  101 MET cc_start: 0.8537 (mmt) cc_final: 0.8178 (mmt)
  outliers start: 5
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0613
  time to fit residues: 1.9995
Evaluate side-chains
  14 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  298 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0010
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.063450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.054851 restraints weight = 11684.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 3.33
r_work: 0.3050 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2557  Z= 0.121
  Angle     :  0.579   6.486   3500  Z= 0.288
  Chirality :  0.039   0.110    443
  Planarity :  0.005   0.044    409
  Dihedral  :  4.095  42.086    344
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.48 %
    Favored  : 86.30 %
  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: -1.91 (0.46), residues: 312
  helix: -0.71 (0.32), residues: 240
  sheet:  None (None), residues: 0
  loop : -2.76 (0.74), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 250 
 TYR   0.013   0.001   TYR A 110 
 PHE   0.009   0.001   PHE A 385 
 TRP   0.011   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2557)
  covalent geometry    : angle       0.57853 ( 3500)
  hydrogen bonds       : bond        0.03419 (  142)
  hydrogen bonds       : angle       4.05939 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  101 MET cc_start: 0.9144 (mmt) cc_final: 0.8661 (mmm)
REVERT: A  285 GLN cc_start: 0.9046 (pm20) cc_final: 0.8797 (pm20)
REVERT: A  439 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7234 (t80)
REVERT: A  450 PHE cc_start: 0.8130 (m-10) cc_final: 0.7920 (m-10)
  outliers start: 6
  outliers final: 2
  residues processed: 20
  average time/residue: 0.0497
  time to fit residues: 1.3406
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  439 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
A 287 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.061990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.053063 restraints weight = 12123.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 3.46
r_work: 0.2997 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2557  Z= 0.134
  Angle     :  0.563   7.561   3500  Z= 0.275
  Chirality :  0.039   0.110    443
  Planarity :  0.004   0.046    409
  Dihedral  :  3.549  29.137    343
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.85 %
    Favored  : 85.93 %
  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: -0.86 (0.50), residues: 312
  helix:  0.07 (0.35), residues: 244
  sheet:  None (None), residues: 0
  loop : -2.63 (0.79), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.006   0.001   TYR A 135 
 PHE   0.011   0.001   PHE A 385 
 TRP   0.013   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 2557)
  covalent geometry    : angle       0.56313 ( 3500)
  hydrogen bonds       : bond        0.03075 (  142)
  hydrogen bonds       : angle       3.63808 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.055 
Fit side-chains
REVERT: A  439 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7270 (t80)
  outliers start: 6
  outliers final: 2
  residues processed: 19
  average time/residue: 0.0423
  time to fit residues: 1.0864
Evaluate side-chains
  15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.2166

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.061708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.052685 restraints weight = 12264.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 3.51
r_work: 0.2977 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2557  Z= 0.140
  Angle     :  0.567   6.811   3500  Z= 0.278
  Chirality :  0.039   0.108    443
  Planarity :  0.004   0.046    409
  Dihedral  :  3.191  12.907    341
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.44 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.19 (0.51), residues: 312
  helix:  0.49 (0.35), residues: 246
  sheet:  None (None), residues: 0
  loop : -2.25 (0.82), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 296 
 TYR   0.005   0.001   TYR A 135 
 PHE   0.011   0.001   PHE A 385 
 TRP   0.011   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2557)
  covalent geometry    : angle       0.56660 ( 3500)
  hydrogen bonds       : bond        0.02819 (  142)
  hydrogen bonds       : angle       3.47983 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 14
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7962 (pm20)
REVERT: A  439 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7213 (t80)
  outliers start: 5
  outliers final: 2
  residues processed: 18
  average time/residue: 0.0647
  time to fit residues: 1.4357
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.061770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.052874 restraints weight = 11923.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 3.41
r_work: 0.2982 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2557  Z= 0.118
  Angle     :  0.556   8.361   3500  Z= 0.270
  Chirality :  0.039   0.114    443
  Planarity :  0.004   0.048    409
  Dihedral  :  3.129  13.666    341
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.56 %
    Favored  : 81.85 %
  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:  0.16 (0.51), residues: 312
  helix:  0.72 (0.35), residues: 247
  sheet:  None (None), residues: 0
  loop : -2.07 (0.81), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 296 
 TYR   0.006   0.001   TYR A 135 
 PHE   0.015   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2557)
  covalent geometry    : angle       0.55621 ( 3500)
  hydrogen bonds       : bond        0.02663 (  142)
  hydrogen bonds       : angle       3.42499 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 15
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7939 (pm20)
REVERT: A  439 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7239 (t80)
  outliers start: 7
  outliers final: 2
  residues processed: 21
  average time/residue: 0.0596
  time to fit residues: 1.5618
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3365 r_free = 0.3365 target = 0.062177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.053189 restraints weight = 12150.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 3.51
r_work: 0.2998 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2557  Z= 0.114
  Angle     :  0.565   8.280   3500  Z= 0.274
  Chirality :  0.039   0.123    443
  Planarity :  0.004   0.048    409
  Dihedral  :  3.155  13.571    341
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.41 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.44 (0.51), residues: 312
  helix:  0.88 (0.35), residues: 246
  sheet:  None (None), residues: 0
  loop : -1.81 (0.85), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.005   0.001   TYR A 135 
 PHE   0.011   0.001   PHE A 385 
 TRP   0.009   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2557)
  covalent geometry    : angle       0.56534 ( 3500)
  hydrogen bonds       : bond        0.02502 (  142)
  hydrogen bonds       : angle       3.40735 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7943 (pm20)
REVERT: A  270 MET cc_start: 0.8903 (ttm) cc_final: 0.8518 (mtt)
REVERT: A  278 MET cc_start: 0.8730 (ptp) cc_final: 0.8389 (ptp)
REVERT: A  439 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7279 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 18
  average time/residue: 0.0527
  time to fit residues: 1.2559
Evaluate side-chains
  18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Chi-restraints excluded: chain A residue  452 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0980
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0000
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7788

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.062578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.053709 restraints weight = 11842.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.39
r_work: 0.3014 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2557  Z= 0.115
  Angle     :  0.554   8.908   3500  Z= 0.266
  Chirality :  0.039   0.110    443
  Planarity :  0.003   0.049    409
  Dihedral  :  3.136  13.359    341
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.67 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.65 (0.51), residues: 312
  helix:  1.04 (0.35), residues: 245
  sheet:  None (None), residues: 0
  loop : -1.74 (0.85), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.007   0.001   TYR A 135 
 PHE   0.011   0.001   PHE A 385 
 TRP   0.010   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2557)
  covalent geometry    : angle       0.55387 ( 3500)
  hydrogen bonds       : bond        0.02526 (  142)
  hydrogen bonds       : angle       3.38606 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 13
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7950 (pm20)
REVERT: A  278 MET cc_start: 0.8888 (ptp) cc_final: 0.8534 (ptp)
REVERT: A  439 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7331 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 19
  average time/residue: 0.0592
  time to fit residues: 1.4761
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Chi-restraints excluded: chain A residue  452 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0170
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.0020

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.062257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.053118 restraints weight = 12057.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 3.48
r_work: 0.2995 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2557  Z= 0.126
  Angle     :  0.580   8.596   3500  Z= 0.278
  Chirality :  0.039   0.122    443
  Planarity :  0.004   0.049    409
  Dihedral  :  3.192  13.688    341
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.41 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.85 (0.51), residues: 312
  helix:  1.17 (0.35), residues: 245
  sheet:  None (None), residues: 0
  loop : -1.62 (0.85), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 296 
 TYR   0.006   0.001   TYR A 135 
 PHE   0.020   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 2557)
  covalent geometry    : angle       0.57957 ( 3500)
  hydrogen bonds       : bond        0.02553 (  142)
  hydrogen bonds       : angle       3.38215 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7954 (pm20)
REVERT: A  270 MET cc_start: 0.8949 (ttm) cc_final: 0.8649 (mtt)
REVERT: A  278 MET cc_start: 0.8890 (ptp) cc_final: 0.8547 (ptp)
REVERT: A  439 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7344 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 18
  average time/residue: 0.0727
  time to fit residues: 1.6234
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Chi-restraints excluded: chain A residue  452 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.060474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.051420 restraints weight = 12501.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.55
r_work: 0.2922 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2557  Z= 0.144
  Angle     :  0.594   9.424   3500  Z= 0.284
  Chirality :  0.040   0.111    443
  Planarity :  0.004   0.049    409
  Dihedral  :  3.283  13.531    341
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.41 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.89 (0.51), residues: 312
  helix:  1.20 (0.35), residues: 245
  sheet:  None (None), residues: 0
  loop : -1.59 (0.83), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.009   0.001   TYR A 135 
 PHE   0.021   0.001   PHE A 450 
 TRP   0.011   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2557)
  covalent geometry    : angle       0.59391 ( 3500)
  hydrogen bonds       : bond        0.02758 (  142)
  hydrogen bonds       : angle       3.43915 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7952 (pm20)
REVERT: A  270 MET cc_start: 0.8948 (ttm) cc_final: 0.8661 (mtt)
REVERT: A  278 MET cc_start: 0.9033 (ptp) cc_final: 0.8695 (ptp)
REVERT: A  439 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7293 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 17
  average time/residue: 0.0588
  time to fit residues: 1.3255
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Chi-restraints excluded: chain A residue  452 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3328 r_free = 0.3328 target = 0.061050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.052100 restraints weight = 12307.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 3.50
r_work: 0.2946 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2557  Z= 0.117
  Angle     :  0.572   9.542   3500  Z= 0.273
  Chirality :  0.039   0.112    443
  Planarity :  0.004   0.048    409
  Dihedral  :  3.199  13.917    341
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.78 %
    Favored  : 80.37 %
  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:  0.91 (0.51), residues: 312
  helix:  1.21 (0.35), residues: 245
  sheet:  None (None), residues: 0
  loop : -1.57 (0.84), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.007   0.001   TYR A 135 
 PHE   0.020   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 2557)
  covalent geometry    : angle       0.57212 ( 3500)
  hydrogen bonds       : bond        0.02550 (  142)
  hydrogen bonds       : angle       3.37965 (  420)

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

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

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  624 Ramachandran restraints generated.
    312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7942 (pm20)
REVERT: A  270 MET cc_start: 0.8941 (ttm) cc_final: 0.8652 (mtt)
REVERT: A  278 MET cc_start: 0.8994 (ptp) cc_final: 0.8645 (ptp)
REVERT: A  439 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7364 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 17
  average time/residue: 0.0583
  time to fit residues: 1.3230
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  439 TYR
Chi-restraints excluded: chain A residue  452 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 10 optimal weight:    0.0470
   chunk 25 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5078

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.062222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.053272 restraints weight = 12208.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 3.55
r_work: 0.3005 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2557  Z= 0.101
  Angle     :  0.548   9.463   3500  Z= 0.262
  Chirality :  0.038   0.115    443
  Planarity :  0.004   0.048    409
  Dihedral  :  3.055  13.732    341
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.78 %
    Favored  : 80.37 %
  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:  1.00 (0.51), residues: 312
  helix:  1.29 (0.35), residues: 245
  sheet:  None (None), residues: 0
  loop : -1.60 (0.83), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.007   0.000   TYR A 135 
 PHE   0.020   0.001   PHE A 450 
 TRP   0.010   0.001   TRP A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2557)
  covalent geometry    : angle       0.54825 ( 3500)
  hydrogen bonds       : bond        0.02294 (  142)
  hydrogen bonds       : angle       3.27581 (  420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 733.42 seconds
wall clock time: 13 minutes 15.39 seconds (795.39 seconds total)