Starting phenix.real_space_refine
on Fri Aug 22 20:37:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r9k_24328/08_2025/7r9k_24328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r9k_24328/08_2025/7r9k_24328.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r9k_24328/08_2025/7r9k_24328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r9k_24328/08_2025/7r9k_24328.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r9k_24328/08_2025/7r9k_24328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r9k_24328/08_2025/7r9k_24328.map"
  }
  resolution = 4.1
  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: 5
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2351      2.51       5
     N     655      2.21       5
     O     759      1.98       5
     H    3938      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7726
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7726
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 1.34, per 1000 atoms: 0.17
  Number of scatterers: 7726
  At special positions: 0
  Unit cell: (75.6, 77.76, 104.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     O     759      8.00
     N     655      7.00
     C    2351      6.00
     H    3938      1.00
    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: 0.51
  Conformation dependent library (CDL) restraints added in 299.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  938

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 4 sheets defined
      54.3% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'J' and resid 20 through 35
      removed outlier: 3.862A  pdb=" N   LEU J  26 " --> pdb=" O   ARG J  22 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY J  28 " --> pdb=" O   ASN J  24 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE J  31 " --> pdb=" O   ALA J  27 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL J  35 " --> pdb=" O   ILE J  31 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 61 through 66
    Processing helix  chain 'J' and resid 75 through 89
      removed outlier: 3.896A  pdb=" N   ILE J  79 " --> pdb=" O   ALA J  75 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL J  81 " --> pdb=" O   MET J  77 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA J  82 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS J  87 " --> pdb=" O   LYS J  83 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU J  88 " --> pdb=" O   THR J  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 113
      removed outlier: 3.842A  pdb=" N   ALA J  96 " --> pdb=" O   GLY J  92 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL J  97 " --> pdb=" O   THR J  93 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA J 100 " --> pdb=" O   ALA J  96 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU J 103 " --> pdb=" O   VAL J  99 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN J 113 " --> pdb=" O   GLU J 109 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.795A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL J 121 " --> pdb=" O   PRO J 117 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS J 122 " --> pdb=" O   THR J 118 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS J 136 " --> pdb=" O   GLN J 132 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE J 138 " --> pdb=" O   LEU J 134 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 148 through 162
      removed outlier: 3.960A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET J 155 " --> pdb=" O   THR J 151 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR J 156 " --> pdb=" O   LYS J 152 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER J 157 " --> pdb=" O   ILE J 153 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LYS J 161 " --> pdb=" O   SER J 157 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY J 162 " --> pdb=" O   ILE J 158 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 167 through 182
      removed outlier: 4.097A  pdb=" N   GLU J 172 " --> pdb=" O   GLU J 168 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA J 180 " --> pdb=" O   GLU J 176 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL J 181 " --> pdb=" O   ALA J 177 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL J 182 " --> pdb=" O   VAL J 178 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 202 through 206
      removed outlier: 3.543A  pdb=" N   ASP J 205 " --> pdb=" O   SER J 202 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 271
      removed outlier: 3.799A  pdb=" N   GLU J 260 " --> pdb=" O   ALA J 256 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE J 261 " --> pdb=" O   LYS J 257 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   ILE J 262 " --> pdb=" O   LEU J 258 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 271 through 279
      removed outlier: 3.691A  pdb=" N   GLU J 275 " --> pdb=" O   ASP J 271 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   SER J 279 " --> pdb=" O   GLU J 275 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 291 through 302
      removed outlier: 3.989A  pdb=" N   HIS J 296 " --> pdb=" O   ASP J 292 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 322
      removed outlier: 3.723A  pdb=" N   MET J 314 " --> pdb=" O   LYS J 310 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU J 315 " --> pdb=" O   LYS J 311 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA J 318 " --> pdb=" O   MET J 314 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 398
      removed outlier: 4.552A  pdb=" N   GLU J 379 " --> pdb=" O   HIS J 375 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL J 380 " --> pdb=" O   VAL J 376 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ARG J 382 " --> pdb=" O   GLU J 378 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA J 383 " --> pdb=" O   GLU J 379 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP J 385 " --> pdb=" O   ALA J 381 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL J 388 " --> pdb=" O   VAL J 384 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY J 389 " --> pdb=" O   ASP J 385 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR J 394 " --> pdb=" O   VAL J 390 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 405 through 422
      removed outlier: 3.836A  pdb=" N   GLU J 410 " --> pdb=" O   SER J 406 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU J 411 " --> pdb=" O   THR J 407 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER J 412 " --> pdb=" O   GLU J 408 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG J 416 " --> pdb=" O   SER J 412 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TYR J 418 " --> pdb=" O   LYS J 414 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLY J 421 " --> pdb=" O   GLU J 417 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE J 422 " --> pdb=" O   TYR J 418 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 425 through 438
      removed outlier: 3.806A  pdb=" N   ALA J 429 " --> pdb=" O   ARG J 425 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 439 through 447
      removed outlier: 3.559A  pdb=" N   THR J 443 " --> pdb=" O   VAL J 439 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA J 445 " --> pdb=" O   PRO J 441 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 453 through 463
      removed outlier: 3.605A  pdb=" N   VAL J 457 " --> pdb=" O   ILE J 453 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LYS J 458 " --> pdb=" O   GLU J 454 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 482 through 487
      removed outlier: 3.974A  pdb=" N   ASN J 486 " --> pdb=" O   ASP J 482 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY J 487 " --> pdb=" O   MET J 483 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 482 through 487'
    Processing helix  chain 'J' and resid 492 through 512
      removed outlier: 3.693A  pdb=" N   GLN J 497 " --> pdb=" O   ARG J 493 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU J 504 " --> pdb=" O   GLN J 500 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU J 509 " --> pdb=" O   SER J 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 49
      removed outlier: 4.251A  pdb=" N   LYS J  46 " --> pdb=" O   THR J  58 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   THR J  58 " --> pdb=" O   LYS J  46 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL J  56 " --> pdb=" O   LEU J  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 140 through 141
    Processing sheet with id=AA3, first strand: chain 'J' and resid 193 through 197
      removed outlier: 7.115A  pdb=" N   LYS J 194 " --> pdb=" O   MET J 367 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   ILE J 369 " --> pdb=" O   LYS J 194 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLU J 196 " --> pdb=" O   ILE J 369 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU J 368 " --> pdb=" O   GLU J 207 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLU J 207 " --> pdb=" O   LEU J 368 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 226 through 228
      removed outlier: 3.504A  pdb=" N   VAL J 227 " --> pdb=" O   VAL J 343 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU J 342 " --> pdb=" O   GLU J 357 " (cutoff:3.500A)

    138 hydrogen bonds defined for protein.
    405 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3931
        1.03 -     1.23: 7
        1.23 -     1.42: 1405
        1.42 -     1.61: 2365
        1.61 -     1.81: 39
  Bond restraints: 7747
  Sorted by residual:
  bond pdb=" C   ILE J 239 "
       pdb=" N   GLU J 240 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 1.40e-02 5.10e+03 2.71e-01
  bond pdb=" NE  ARG J 431 "
       pdb=" CZ  ARG J 431 "
    ideal  model  delta    sigma   weight residual
    1.326  1.331 -0.005 1.10e-02 8.26e+03 2.33e-01
  bond pdb=" C   VAL J 439 "
       pdb=" O   VAL J 439 "
    ideal  model  delta    sigma   weight residual
    1.236  1.242 -0.006 1.19e-02 7.06e+03 2.31e-01
  bond pdb=" C   ILE J 440 "
       pdb=" N   PRO J 441 "
    ideal  model  delta    sigma   weight residual
    1.337  1.343 -0.006 1.24e-02 6.50e+03 2.25e-01
  bond pdb=" CB  PRO J 441 "
       pdb=" CG  PRO J 441 "
    ideal  model  delta    sigma   weight residual
    1.492  1.471  0.021 5.00e-02 4.00e+02 1.82e-01
  ... (remaining 7742 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 13631
        1.13 -     2.25: 499
        2.25 -     3.38: 10
        3.38 -     4.50: 4
        4.50 -     5.63: 1
  Bond angle restraints: 14145
  Sorted by residual:
  angle pdb=" CA  VAL J 439 "
        pdb=" C   VAL J 439 "
        pdb=" N   ILE J 440 "
      ideal   model   delta    sigma   weight residual
     116.60  119.38   -2.78 1.45e+00 4.76e-01 3.68e+00
  angle pdb=" N   VAL J 439 "
        pdb=" CA  VAL J 439 "
        pdb=" C   VAL J 439 "
      ideal   model   delta    sigma   weight residual
     109.34  113.02   -3.68 2.08e+00 2.31e-01 3.13e+00
  angle pdb=" CA  ALA J 201 "
        pdb=" C   ALA J 201 "
        pdb=" N   SER J 202 "
      ideal   model   delta    sigma   weight residual
     116.84  119.75   -2.91 1.71e+00 3.42e-01 2.89e+00
  angle pdb=" N   ALA J 201 "
        pdb=" CA  ALA J 201 "
        pdb=" C   ALA J 201 "
      ideal   model   delta    sigma   weight residual
     110.80  114.32   -3.52 2.13e+00 2.20e-01 2.73e+00
  angle pdb=" N   GLU J 240 "
        pdb=" CA  GLU J 240 "
        pdb=" C   GLU J 240 "
      ideal   model   delta    sigma   weight residual
     110.80  107.34    3.46 2.13e+00 2.20e-01 2.63e+00
  ... (remaining 14140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.94: 3333
       11.94 -    23.88: 124
       23.88 -    35.82: 35
       35.82 -    47.76: 22
       47.76 -    59.70: 22
  Dihedral angle restraints: 3536
    sinusoidal: 2036
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  LEU J 258 "
           pdb=" CB  LEU J 258 "
           pdb=" CG  LEU J 258 "
           pdb=" CD1 LEU J 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.07   40.93     3      1.50e+01 4.44e-03 7.31e+00
  dihedral pdb=" CA  LEU J 135 "
           pdb=" CB  LEU J 135 "
           pdb=" CG  LEU J 135 "
           pdb=" CD1 LEU J 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  144.83   35.17     3      1.50e+01 4.44e-03 6.01e+00
  dihedral pdb=" CA  LYS J 347 "
           pdb=" CB  LYS J 347 "
           pdb=" CG  LYS J 347 "
           pdb=" CD  LYS J 347 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   90.68  -30.68     3      1.50e+01 4.44e-03 4.91e+00
  ... (remaining 3533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 405
       0.024 -    0.048: 126
       0.048 -    0.072: 51
       0.072 -    0.096: 22
       0.096 -    0.120: 26
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ILE J 303 "
            pdb=" N   ILE J 303 "
            pdb=" C   ILE J 303 "
            pdb=" CB  ILE J 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  VAL J 188 "
            pdb=" N   VAL J 188 "
            pdb=" C   VAL J 188 "
            pdb=" CB  VAL J 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  ILE J 195 "
            pdb=" N   ILE J 195 "
            pdb=" C   ILE J 195 "
            pdb=" CB  ILE J 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.47e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.006 5.00e-02 4.00e+02   9.72e-03 1.51e-01
        pdb=" N   PRO J 255 "    0.017 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J 255 "   -0.005 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET J 223 "    0.006 5.00e-02 4.00e+02   9.06e-03 1.31e-01
        pdb=" N   PRO J 224 "   -0.016 5.00e-02 4.00e+02
        pdb=" CA  PRO J 224 "    0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J 224 "    0.005 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY J  40 "    0.005 5.00e-02 4.00e+02   8.20e-03 1.08e-01
        pdb=" N   PRO J  41 "   -0.014 5.00e-02 4.00e+02
        pdb=" CA  PRO J  41 "    0.004 5.00e-02 4.00e+02
        pdb=" CD  PRO J  41 "    0.005 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 543
        2.24 -     2.83: 17924
        2.83 -     3.42: 17879
        3.42 -     4.01: 23299
        4.01 -     4.60: 36615
  Nonbonded interactions: 96260
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP J 451 "
            pdb=" H   GLU J 454 "
     model   vdw
     1.646 2.450
  nonbonded pdb=" OE1 GLU J 168 "
            pdb=" H   GLU J 168 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" O   LEU J 317 "
            pdb=" HG1 THR J 321 "
     model   vdw
     1.713 2.450
  nonbonded pdb=" OE1 GLU J 245 "
            pdb=" H   GLU J 245 "
     model   vdw
     1.720 2.450
  nonbonded pdb=" OE1 GLU J  33 "
            pdb=" HE  ARG J  36 "
     model   vdw
     1.728 2.450
  ... (remaining 96255 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:             0.050
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.390
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
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   0.021   3809  Z= 0.079
  Angle     :  0.353   5.628   5126  Z= 0.201
  Chirality :  0.037   0.120    630
  Planarity :  0.001   0.010    663
  Dihedral  :  4.651  40.926   1463
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 10.34 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.05 (0.32), residues: 503
  helix: -3.25 (0.22), residues: 193
  sheet: -4.43 (0.45), residues: 62
  loop : -1.55 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 522 
 TYR   0.001   0.000   TYR J 297 
 PHE   0.002   0.000   PHE J 261 
 HIS   0.001   0.000   HIS J 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00155 ( 3809)
  covalent geometry    : angle       0.35260 ( 5126)
  hydrogen bonds       : bond        0.35772 (  138)
  hydrogen bonds       : angle       8.55419 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1562
  time to fit residues: 9.5580
Evaluate side-chains
  29 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
J 125 GLN
J 132 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.054758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037209 restraints weight = 75652.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.038606 restraints weight = 36312.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.039481 restraints weight = 22039.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.040065 restraints weight = 15684.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.040425 restraints weight = 12519.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3809  Z= 0.213
  Angle     :  0.574   5.664   5126  Z= 0.319
  Chirality :  0.039   0.126    630
  Planarity :  0.003   0.024    663
  Dihedral  :  2.973  15.984    529
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.92 (0.34), residues: 503
  helix: -1.11 (0.31), residues: 232
  sheet: -3.57 (0.55), residues: 58
  loop : -2.28 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 425 
 TYR   0.012   0.002   TYR J 418 
 PHE   0.004   0.001   PHE J 261 
 HIS   0.003   0.001   HIS J 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 3809)
  covalent geometry    : angle       0.57418 ( 5126)
  hydrogen bonds       : bond        0.05508 (  138)
  hydrogen bonds       : angle       5.07128 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8782 (tp30)
REVERT: J  155 MET cc_start: 0.9704 (mmp) cc_final: 0.9293 (mmm)
REVERT: J  297 TYR cc_start: 0.9422 (m-80) cc_final: 0.9167 (m-80)
REVERT: J  435 ASP cc_start: 0.9474 (m-30) cc_final: 0.9165 (m-30)
REVERT: J  490 GLU cc_start: 0.9361 (pt0) cc_final: 0.9074 (pm20)
REVERT: J  508 MET cc_start: 0.9306 (mmp) cc_final: 0.8948 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1616
  time to fit residues: 6.2014
Evaluate side-chains
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0370
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.053860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.036182 restraints weight = 80797.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.037517 restraints weight = 38279.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.038367 restraints weight = 23078.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.038863 restraints weight = 16700.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.039125 restraints weight = 13589.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3809  Z= 0.161
  Angle     :  0.449   4.547   5126  Z= 0.249
  Chirality :  0.038   0.116    630
  Planarity :  0.002   0.015    663
  Dihedral  :  2.878  15.124    529
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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: -1.82 (0.36), residues: 503
  helix: -0.12 (0.33), residues: 237
  sheet: -2.83 (0.67), residues: 58
  loop : -1.91 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J  22 
 TYR   0.004   0.001   TYR J 418 
 PHE   0.006   0.001   PHE J 261 
 HIS   0.003   0.001   HIS J 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3809)
  covalent geometry    : angle       0.44917 ( 5126)
  hydrogen bonds       : bond        0.04325 (  138)
  hydrogen bonds       : angle       4.50252 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9668 (mmp) cc_final: 0.9206 (mmm)
REVERT: J  285 PHE cc_start: 0.9355 (m-80) cc_final: 0.8885 (m-80)
REVERT: J  297 TYR cc_start: 0.9415 (m-80) cc_final: 0.9134 (m-80)
REVERT: J  435 ASP cc_start: 0.9493 (m-30) cc_final: 0.9212 (m-30)
REVERT: J  454 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8991 (mm-30)
REVERT: J  490 GLU cc_start: 0.9295 (pt0) cc_final: 0.9088 (pm20)
REVERT: J  508 MET cc_start: 0.9372 (mmp) cc_final: 0.9015 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1361
  time to fit residues: 4.3108
Evaluate side-chains
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0770
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.3744

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.053789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.035821 restraints weight = 79961.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.037174 restraints weight = 38276.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.038040 restraints weight = 23412.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.038536 restraints weight = 16749.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.038871 restraints weight = 13753.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3809  Z= 0.165
  Angle     :  0.439   4.169   5126  Z= 0.245
  Chirality :  0.038   0.115    630
  Planarity :  0.002   0.019    663
  Dihedral  :  3.017  13.119    529
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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: -1.33 (0.37), residues: 503
  helix:  0.26 (0.33), residues: 240
  sheet: -2.58 (0.70), residues: 58
  loop : -1.67 (0.42), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 346 
 TYR   0.005   0.001   TYR J 418 
 PHE   0.004   0.001   PHE J 261 
 HIS   0.004   0.001   HIS J 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3809)
  covalent geometry    : angle       0.43941 ( 5126)
  hydrogen bonds       : bond        0.03314 (  138)
  hydrogen bonds       : angle       4.23871 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9667 (mmp) cc_final: 0.9220 (mmm)
REVERT: J  285 PHE cc_start: 0.9384 (m-80) cc_final: 0.8864 (m-80)
REVERT: J  435 ASP cc_start: 0.9481 (m-30) cc_final: 0.9188 (m-30)
REVERT: J  454 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9054 (mm-30)
REVERT: J  490 GLU cc_start: 0.9235 (pt0) cc_final: 0.8930 (pm20)
REVERT: J  508 MET cc_start: 0.9420 (mmp) cc_final: 0.9120 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1352
  time to fit residues: 4.1034
Evaluate side-chains
  21 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.053595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.035728 restraints weight = 79220.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.037063 restraints weight = 37663.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.037912 restraints weight = 22969.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.038405 restraints weight = 16471.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.038747 restraints weight = 13585.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.5033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3809  Z= 0.123
  Angle     :  0.391   4.201   5126  Z= 0.217
  Chirality :  0.038   0.121    630
  Planarity :  0.002   0.017    663
  Dihedral  :  2.931  12.932    529
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.38), residues: 503
  helix:  0.63 (0.34), residues: 240
  sheet: -2.33 (0.72), residues: 58
  loop : -1.52 (0.42), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 346 
 TYR   0.004   0.001   TYR J 297 
 PHE   0.005   0.001   PHE J 261 
 HIS   0.001   0.000   HIS J 463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3809)
  covalent geometry    : angle       0.39051 ( 5126)
  hydrogen bonds       : bond        0.03081 (  138)
  hydrogen bonds       : angle       4.09230 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9666 (mmp) cc_final: 0.9191 (mmm)
REVERT: J  285 PHE cc_start: 0.9403 (m-80) cc_final: 0.8889 (m-80)
REVERT: J  435 ASP cc_start: 0.9483 (m-30) cc_final: 0.9197 (m-30)
REVERT: J  454 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9057 (mm-30)
REVERT: J  490 GLU cc_start: 0.9205 (pt0) cc_final: 0.8898 (pm20)
REVERT: J  508 MET cc_start: 0.9418 (mmp) cc_final: 0.9038 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1337
  time to fit residues: 4.0793
Evaluate side-chains
  21 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0370
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.2664

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

Flipped N/Q/H residues before XYZ refinement:
J  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.053400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.035656 restraints weight = 78990.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.037001 restraints weight = 37334.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.037827 restraints weight = 23004.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.038283 restraints weight = 16538.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.038593 restraints weight = 13770.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.5440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3809  Z= 0.153
  Angle     :  0.418   4.207   5126  Z= 0.235
  Chirality :  0.038   0.115    630
  Planarity :  0.002   0.016    663
  Dihedral  :  3.063  12.600    529
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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: -0.79 (0.38), residues: 503
  helix:  0.66 (0.34), residues: 240
  sheet: -2.20 (0.72), residues: 58
  loop : -1.38 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 346 
 TYR   0.004   0.001   TYR J 418 
 PHE   0.005   0.001   PHE J 261 
 HIS   0.002   0.001   HIS J 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3809)
  covalent geometry    : angle       0.41787 ( 5126)
  hydrogen bonds       : bond        0.02965 (  138)
  hydrogen bonds       : angle       4.06291 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9679 (mmp) cc_final: 0.9223 (mmm)
REVERT: J  285 PHE cc_start: 0.9421 (m-80) cc_final: 0.8926 (m-80)
REVERT: J  435 ASP cc_start: 0.9473 (m-30) cc_final: 0.9201 (m-30)
REVERT: J  490 GLU cc_start: 0.9160 (pt0) cc_final: 0.8851 (pm20)
REVERT: J  508 MET cc_start: 0.9441 (mmp) cc_final: 0.9067 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1421
  time to fit residues: 3.8989
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.053818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.036116 restraints weight = 76974.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.037491 restraints weight = 36315.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.038343 restraints weight = 22026.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.038848 restraints weight = 15800.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.039165 restraints weight = 12866.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3809  Z= 0.111
  Angle     :  0.382   4.139   5126  Z= 0.212
  Chirality :  0.037   0.128    630
  Planarity :  0.002   0.017    663
  Dihedral  :  2.970  12.144    529
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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: -0.52 (0.38), residues: 503
  helix:  0.94 (0.34), residues: 239
  sheet: -2.16 (0.70), residues: 58
  loop : -1.27 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 346 
 TYR   0.004   0.001   TYR J 297 
 PHE   0.004   0.001   PHE J 261 
 HIS   0.001   0.000   HIS J 463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 3809)
  covalent geometry    : angle       0.38172 ( 5126)
  hydrogen bonds       : bond        0.02789 (  138)
  hydrogen bonds       : angle       3.87476 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9679 (mmp) cc_final: 0.9228 (mmm)
REVERT: J  285 PHE cc_start: 0.9401 (m-80) cc_final: 0.8906 (m-80)
REVERT: J  435 ASP cc_start: 0.9463 (m-30) cc_final: 0.9178 (m-30)
REVERT: J  490 GLU cc_start: 0.9172 (pt0) cc_final: 0.8848 (pm20)
REVERT: J  508 MET cc_start: 0.9427 (mmp) cc_final: 0.9044 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1220
  time to fit residues: 3.6024
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.053596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.035726 restraints weight = 78993.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.037082 restraints weight = 37515.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.037921 restraints weight = 22760.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.038445 restraints weight = 16338.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.038735 restraints weight = 13255.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.5783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3809  Z= 0.125
  Angle     :  0.395   4.213   5126  Z= 0.219
  Chirality :  0.037   0.118    630
  Planarity :  0.002   0.018    663
  Dihedral  :  3.019  12.065    529
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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: -0.41 (0.39), residues: 503
  helix:  0.97 (0.34), residues: 239
  sheet: -1.97 (0.73), residues: 58
  loop : -1.17 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 346 
 TYR   0.004   0.001   TYR J 297 
 PHE   0.005   0.001   PHE J 261 
 HIS   0.001   0.000   HIS J 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3809)
  covalent geometry    : angle       0.39457 ( 5126)
  hydrogen bonds       : bond        0.02705 (  138)
  hydrogen bonds       : angle       3.84000 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9683 (mmp) cc_final: 0.9232 (mmm)
REVERT: J  435 ASP cc_start: 0.9464 (m-30) cc_final: 0.9185 (m-30)
REVERT: J  490 GLU cc_start: 0.9132 (pt0) cc_final: 0.8824 (pm20)
REVERT: J  508 MET cc_start: 0.9450 (mmp) cc_final: 0.9077 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1064
  time to fit residues: 2.9661
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.053329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.035887 restraints weight = 78327.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.037234 restraints weight = 36878.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.038047 restraints weight = 22294.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.038528 restraints weight = 16098.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.038821 restraints weight = 13148.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.6072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3809  Z= 0.178
  Angle     :  0.444   4.323   5126  Z= 0.250
  Chirality :  0.038   0.117    630
  Planarity :  0.002   0.028    663
  Dihedral  :  3.250  13.190    529
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.38), residues: 503
  helix:  0.75 (0.33), residues: 239
  sheet: -2.08 (0.78), residues: 52
  loop : -1.04 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 346 
 TYR   0.004   0.001   TYR J 297 
 PHE   0.004   0.001   PHE J 261 
 HIS   0.002   0.001   HIS J  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3809)
  covalent geometry    : angle       0.44441 ( 5126)
  hydrogen bonds       : bond        0.02908 (  138)
  hydrogen bonds       : angle       4.06431 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9692 (mmp) cc_final: 0.9175 (mmm)
REVERT: J  435 ASP cc_start: 0.9482 (m-30) cc_final: 0.9232 (m-30)
REVERT: J  490 GLU cc_start: 0.9096 (pt0) cc_final: 0.8818 (pm20)
REVERT: J  508 MET cc_start: 0.9475 (mmp) cc_final: 0.9115 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1396
  time to fit residues: 4.0776
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.053615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.035761 restraints weight = 78361.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.037117 restraints weight = 36898.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.037931 restraints weight = 22565.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.038421 restraints weight = 16448.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.038699 restraints weight = 13464.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.6140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3809  Z= 0.122
  Angle     :  0.393   4.154   5126  Z= 0.219
  Chirality :  0.037   0.122    630
  Planarity :  0.002   0.029    663
  Dihedral  :  3.152  13.390    529
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.38), residues: 503
  helix:  0.96 (0.34), residues: 239
  sheet: -1.82 (0.75), residues: 58
  loop : -1.14 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 346 
 TYR   0.004   0.001   TYR J 297 
 PHE   0.004   0.001   PHE J 261 
 HIS   0.001   0.000   HIS J 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3809)
  covalent geometry    : angle       0.39349 ( 5126)
  hydrogen bonds       : bond        0.02693 (  138)
  hydrogen bonds       : angle       3.83589 (  405)

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9680 (mmp) cc_final: 0.9210 (mmm)
REVERT: J  353 MET cc_start: 0.9399 (mpp) cc_final: 0.9091 (mpp)
REVERT: J  435 ASP cc_start: 0.9471 (m-30) cc_final: 0.9205 (m-30)
REVERT: J  490 GLU cc_start: 0.9105 (pt0) cc_final: 0.8815 (pm20)
REVERT: J  508 MET cc_start: 0.9460 (mmp) cc_final: 0.9105 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1343
  time to fit residues: 3.7014
Evaluate side-chains
  20 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0370
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0070
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.4278

-------------------------------------------------------------------------------
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 = 0.053810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.036341 restraints weight = 76897.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.037682 restraints weight = 36352.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.038514 restraints weight = 21989.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.039044 restraints weight = 15744.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.039324 restraints weight = 12722.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3809  Z= 0.073
  Angle     :  0.363   4.016   5126  Z= 0.197
  Chirality :  0.038   0.123    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.885  11.366    529
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.39), residues: 503
  helix:  1.44 (0.35), residues: 239
  sheet: -1.64 (0.71), residues: 68
  loop : -1.05 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 370 
 TYR   0.003   0.000   TYR J 297 
 PHE   0.005   0.001   PHE J 261 
 HIS   0.001   0.000   HIS J 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00159 ( 3809)
  covalent geometry    : angle       0.36280 ( 5126)
  hydrogen bonds       : bond        0.02370 (  138)
  hydrogen bonds       : angle       3.51685 (  405)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1754.92 seconds
wall clock time: 30 minutes 33.78 seconds (1833.78 seconds total)