Starting phenix.real_space_refine
on Fri Aug 22 20:31:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r9u_24331/08_2025/7r9u_24331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r9u_24331/08_2025/7r9u_24331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r9u_24331/08_2025/7r9u_24331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r9u_24331/08_2025/7r9u_24331.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r9u_24331/08_2025/7r9u_24331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r9u_24331/08_2025/7r9u_24331.map"
  }
  resolution = 4.4
  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: 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    3939      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 7727
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7727
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 1.30, per 1000 atoms: 0.17
  Number of scatterers: 7727
  At special positions: 0
  Unit cell: (78.84, 72.36, 110.16, 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    3939      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: 0.41
  Conformation dependent library (CDL) restraints added in 245.3 milliseconds
  
  Enol-peptide restraints added in 476.8 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:
      20 helices and 4 sheets defined
      51.7% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'J' and resid 21 through 37
      removed outlier: 4.005A  pdb=" N   ILE J  25 " --> pdb=" O   GLN J  21 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY J  28 " --> pdb=" O   ASN J  24 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG J  29 " --> pdb=" O   ILE J  25 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE J  31 " --> pdb=" O   ALA J  27 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   THR J  34 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL J  35 " --> pdb=" O   ILE J  31 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER J  37 " --> pdb=" O   GLU J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 60 through 68
      removed outlier: 3.932A  pdb=" N   ILE J  64 " --> pdb=" O   ASP J  60 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU J  65 " --> pdb=" O   GLY J  61 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU J  67 " --> pdb=" O   THR J  63 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 76 through 87
      removed outlier: 3.643A  pdb=" N   THR J  84 " --> pdb=" O   GLU J  80 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLN J  85 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLU J  86 " --> pdb=" O   ALA J  82 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS J  87 " --> pdb=" O   LYS J  83 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 93 through 113
      removed outlier: 3.634A  pdb=" N   VAL J  99 " --> pdb=" O   THR J  95 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY J 101 " --> pdb=" O   VAL J  97 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLU J 102 " --> pdb=" O   VAL J  98 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU J 103 " --> pdb=" O   VAL J  99 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLN J 113 " --> pdb=" O   GLU J 109 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.674A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY J 123 " --> pdb=" O   ILE J 119 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN J 132 " --> pdb=" O   ALA J 128 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU J 134 " --> pdb=" O   LYS J 130 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 146 through 159
      removed outlier: 3.608A  pdb=" N   LEU J 150 " --> pdb=" O   ASP J 146 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE J 153 " --> pdb=" O   ILE J 149 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA J 154 " --> pdb=" O   LEU J 150 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   SER J 157 " --> pdb=" O   ILE J 153 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 169 through 181
      removed outlier: 3.562A  pdb=" N   GLU J 176 " --> pdb=" O   GLU J 172 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA J 177 " --> pdb=" O   ILE J 173 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA J 180 " --> pdb=" O   GLU J 176 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL J 181 " --> pdb=" O   ALA J 177 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 202 through 206
      removed outlier: 3.826A  pdb=" N   ASP J 205 " --> pdb=" O   SER J 202 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 260
      removed outlier: 3.711A  pdb=" N   MET J 259 " --> pdb=" O   ALA J 256 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU J 260 " --> pdb=" O   LYS J 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 256 through 260'
    Processing helix  chain 'J' and resid 262 through 279
      removed outlier: 3.787A  pdb=" N   GLU J 266 " --> pdb=" O   ILE J 262 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU J 269 " --> pdb=" O   GLU J 265 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS J 270 " --> pdb=" O   GLU J 266 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 293 through 301
      removed outlier: 4.145A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU J 298 " --> pdb=" O   ALA J 294 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA J 299 " --> pdb=" O   GLN J 295 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 322
      removed outlier: 4.255A  pdb=" N   LYS J 316 " --> pdb=" O   SER J 312 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR J 321 " --> pdb=" O   LEU J 317 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 398
      removed outlier: 3.576A  pdb=" N   ALA J 383 " --> pdb=" O   GLU J 379 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP J 385 " --> pdb=" O   ALA J 381 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP J 386 " --> pdb=" O   ARG J 382 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL J 388 " --> pdb=" O   VAL J 384 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY J 389 " --> pdb=" O   ASP J 385 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   THR J 394 " --> pdb=" O   VAL J 390 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 406 through 420
      removed outlier: 3.504A  pdb=" N   LEU J 411 " --> pdb=" O   THR J 407 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS J 414 " --> pdb=" O   GLU J 410 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ARG J 416 " --> pdb=" O   SER J 412 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU J 420 " --> pdb=" O   ARG J 416 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 423 through 425
      No H-bonds generated for 'chain 'J' and resid 423 through 425'
    Processing helix  chain 'J' and resid 426 through 435
    Processing helix  chain 'J' and resid 438 through 449
      removed outlier: 3.671A  pdb=" N   ARG J 442 " --> pdb=" O   GLU J 438 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU J 444 " --> pdb=" O   ILE J 440 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 454 through 463
      removed outlier: 3.955A  pdb=" N   LYS J 458 " --> pdb=" O   GLU J 454 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ARG J 460 " --> pdb=" O   LEU J 456 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA J 461 " --> pdb=" O   VAL J 457 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA J 462 " --> pdb=" O   LYS J 458 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   HIS J 463 " --> pdb=" O   VAL J 459 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 483 through 487
      removed outlier: 3.560A  pdb=" N   GLY J 487 " --> pdb=" O   MET J 483 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 483 through 487'
    Processing helix  chain 'J' and resid 492 through 511
      removed outlier: 3.628A  pdb=" N   THR J 496 " --> pdb=" O   LEU J 492 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA J 498 " --> pdb=" O   VAL J 494 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU J 509 " --> pdb=" O   SER J 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 140 through 141
      removed outlier: 3.760A  pdb=" N   ILE J 400 " --> pdb=" O   CYS J 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 193 through 199
      removed outlier: 6.619A  pdb=" N   LYS J 194 " --> pdb=" O   MET J 367 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ILE J 369 " --> pdb=" O   LYS J 194 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLU J 196 " --> pdb=" O   ILE J 369 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   GLY J 371 " --> pdb=" O   GLU J 196 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS J 198 " --> pdb=" O   GLY J 371 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR J 366 " --> pdb=" O   ILE J 209 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE J 209 " --> pdb=" O   THR J 366 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   LEU J 368 " --> pdb=" O   GLU J 207 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLU J 207 " --> pdb=" O   LEU J 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'J' and resid 212 through 214
      removed outlier: 3.776A  pdb=" N   ARG J 346 " --> pdb=" O   MET J 353 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 471 through 472
      removed outlier: 3.503A  pdb=" N   GLY J 472 " --> pdb=" O   GLU J 481 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU J 481 " --> pdb=" O   GLY J 472 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    121 hydrogen bonds defined for protein.
    351 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: 1.35

  Time building geometry restraints manager: 0.62 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: 3932
        1.03 -     1.23: 7
        1.23 -     1.42: 1405
        1.42 -     1.61: 2365
        1.61 -     1.81: 39
  Bond restraints: 7748
  Sorted by residual:
  bond pdb=" N   GLY J 200 "
       pdb=" CA  GLY J 200 "
    ideal  model  delta    sigma   weight residual
    1.458  1.449  0.009 9.20e-03 1.18e+04 8.92e-01
  bond pdb=" CA  VAL J 219 "
       pdb=" C   VAL J 219 "
    ideal  model  delta    sigma   weight residual
    1.530  1.523  0.007 1.12e-02 7.97e+03 3.91e-01
  bond pdb=" CA  GLY J 200 "
       pdb=" C   GLY J 200 "
    ideal  model  delta    sigma   weight residual
    1.504  1.514 -0.011 1.83e-02 2.99e+03 3.48e-01
  bond pdb=" C   GLY J 200 "
       pdb=" O   GLY J 200 "
    ideal  model  delta    sigma   weight residual
    1.239  1.234  0.005 8.50e-03 1.38e+04 2.97e-01
  bond pdb=" N   LYS J  42 "
       pdb=" CA  LYS J  42 "
    ideal  model  delta    sigma   weight residual
    1.464  1.457  0.006 1.20e-02 6.94e+03 2.91e-01
  ... (remaining 7743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.76: 12657
        0.76 -     1.52: 1432
        1.52 -     2.28: 48
        2.28 -     3.04: 3
        3.04 -     3.80: 7
  Bond angle restraints: 14147
  Sorted by residual:
  angle pdb=" N   VAL J 219 "
        pdb=" CA  VAL J 219 "
        pdb=" C   VAL J 219 "
      ideal   model   delta    sigma   weight residual
     111.91  109.75    2.16 8.90e-01 1.26e+00 5.89e+00
  angle pdb=" N   LYS J 330 "
        pdb=" CA  LYS J 330 "
        pdb=" C   LYS J 330 "
      ideal   model   delta    sigma   weight residual
     112.97  111.17    1.80 1.06e+00 8.90e-01 2.88e+00
  angle pdb=" C   ILE J 262 "
        pdb=" CA  ILE J 262 "
        pdb=" CB  ILE J 262 "
      ideal   model   delta    sigma   weight residual
     111.65  109.45    2.20 1.41e+00 5.03e-01 2.45e+00
  angle pdb=" C   VAL J  62 "
        pdb=" CA  VAL J  62 "
        pdb=" CB  VAL J  62 "
      ideal   model   delta    sigma   weight residual
     112.16  109.66    2.50 1.63e+00 3.76e-01 2.36e+00
  angle pdb=" CA  ILE J 440 "
        pdb=" C   ILE J 440 "
        pdb=" N   PRO J 441 "
      ideal   model   delta    sigma   weight residual
     118.88  120.92   -2.04 1.54e+00 4.22e-01 1.75e+00
  ... (remaining 14142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.86: 3339
       11.86 -    23.72: 121
       23.72 -    35.58: 33
       35.58 -    47.44: 28
       47.44 -    59.30: 16
  Dihedral angle restraints: 3537
    sinusoidal: 2036
      harmonic: 1501
  Sorted by residual:
  dihedral pdb=" CA  LEU J 284 "
           pdb=" CB  LEU J 284 "
           pdb=" CG  LEU J 284 "
           pdb=" CD1 LEU J 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  142.01   37.99     3      1.50e+01 4.44e-03 6.67e+00
  dihedral pdb=" CB  MET J 508 "
           pdb=" CG  MET J 508 "
           pdb=" SD  MET J 508 "
           pdb=" CE  MET J 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   95.72  -35.72     3      1.50e+01 4.44e-03 6.14e+00
  dihedral pdb=" CB  MET J 483 "
           pdb=" CG  MET J 483 "
           pdb=" SD  MET J 483 "
           pdb=" CE  MET J 483 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   92.54  -32.54     3      1.50e+01 4.44e-03 5.37e+00
  ... (remaining 3534 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 376
       0.024 -    0.048: 154
       0.048 -    0.072: 50
       0.072 -    0.097: 18
       0.097 -    0.121: 32
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ILE J 326 "
            pdb=" N   ILE J 326 "
            pdb=" C   ILE J 326 "
            pdb=" CB  ILE J 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  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 3.62e-01
  chirality pdb=" CA  VAL J 214 "
            pdb=" N   VAL J 214 "
            pdb=" C   VAL J 214 "
            pdb=" CB  VAL J 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.011 5.00e-02 4.00e+02   1.68e-02 4.54e-01
        pdb=" N   PRO J 255 "    0.029 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO J 255 "   -0.009 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS J 116 "    0.009 5.00e-02 4.00e+02   1.38e-02 3.03e-01
        pdb=" N   PRO J 117 "   -0.024 5.00e-02 4.00e+02
        pdb=" CA  PRO J 117 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO J 117 "    0.008 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   9.61e-03 1.48e-01
        pdb=" N   PRO J 224 "   -0.017 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
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 526
        2.23 -     2.83: 17885
        2.83 -     3.42: 17716
        3.42 -     4.01: 22870
        4.01 -     4.60: 36498
  Nonbonded interactions: 95495
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU J 168 "
            pdb=" H   GLU J 168 "
     model   vdw
     1.642 2.450
  nonbonded pdb="HD21 ASN J 328 "
            pdb=" OD2 ASP J 331 "
     model   vdw
     1.696 2.450
  nonbonded pdb=" OD1 ASP J 183 "
            pdb=" H   LYS J 187 "
     model   vdw
     1.744 2.450
  nonbonded pdb=" OE1 GLU J 172 "
            pdb=" H   GLU J 172 "
     model   vdw
     1.749 2.450
  nonbonded pdb=" O   LYS J 152 "
            pdb=" HG1 THR J 156 "
     model   vdw
     1.757 2.450
  ... (remaining 95490 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:             1.740
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.670
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
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   0.011   3809  Z= 0.083
  Angle     :  0.342   3.797   5126  Z= 0.205
  Chirality :  0.038   0.121    630
  Planarity :  0.001   0.017    663
  Dihedral  :  4.356  37.994   1463
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  9.15 %
    Favored  : 90.26 %
  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: -4.49 (0.31), residues: 503
  helix: -3.85 (0.20), residues: 184
  sheet: -3.70 (0.54), residues: 57
  loop : -2.04 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 522 
 TYR   0.001   0.000   TYR J 418 
 PHE   0.001   0.000   PHE J 355 
 HIS   0.002   0.000   HIS J  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00152 ( 3809)
  covalent geometry    : angle       0.34180 ( 5126)
  hydrogen bonds       : bond        0.35736 (  121)
  hydrogen bonds       : angle       8.71211 (  351)

*********************** 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
  56 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.194 
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: J  473 LEU cc_start: 0.7573 (tp) cc_final: 0.7188 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1641
  time to fit residues: 11.5308
Evaluate side-chains
  32 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0370
   chunk 2 optimal weight:    0.0370
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
J 328 ASN
J 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.046847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.033594 restraints weight = 104031.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.035000 restraints weight = 52100.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.035965 restraints weight = 31554.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.036646 restraints weight = 21776.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.037047 restraints weight = 16612.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3809  Z= 0.125
  Angle     :  0.485   4.641   5126  Z= 0.269
  Chirality :  0.040   0.136    630
  Planarity :  0.003   0.045    663
  Dihedral  :  2.650  10.256    529
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.17 %
    Favored  : 95.63 %
  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: -3.09 (0.33), residues: 503
  helix: -1.99 (0.30), residues: 213
  sheet: -3.14 (0.53), residues: 59
  loop : -1.62 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 511 
 TYR   0.013   0.002   TYR J 124 
 PHE   0.012   0.002   PHE J 355 
 HIS   0.004   0.001   HIS J 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 3809)
  covalent geometry    : angle       0.48494 ( 5126)
  hydrogen bonds       : bond        0.07400 (  121)
  hydrogen bonds       : angle       5.25634 (  351)

*********************** 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
  38 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.162 
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  353 MET cc_start: 0.9677 (pmm) cc_final: 0.9433 (pmm)
REVERT: J  413 MET cc_start: 0.8960 (mmp) cc_final: 0.8715 (mmm)
REVERT: J  473 LEU cc_start: 0.9554 (tp) cc_final: 0.9265 (tt)
REVERT: J  483 MET cc_start: 0.9499 (mmp) cc_final: 0.9057 (mmm)
REVERT: J  508 MET cc_start: 0.9624 (mmp) cc_final: 0.9334 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1375
  time to fit residues: 6.6299
Evaluate side-chains
  28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 17 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 31 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
J  24 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.046597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.032816 restraints weight = 110797.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.034117 restraints weight = 57460.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.035058 restraints weight = 35848.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.035642 restraints weight = 25286.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.036074 restraints weight = 19993.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3809  Z= 0.107
  Angle     :  0.422   4.289   5126  Z= 0.233
  Chirality :  0.038   0.133    630
  Planarity :  0.002   0.027    663
  Dihedral  :  2.666   9.855    529
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  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: -1.98 (0.35), residues: 503
  helix: -0.90 (0.33), residues: 218
  sheet: -2.20 (0.60), residues: 61
  loop : -1.31 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 382 
 TYR   0.005   0.001   TYR J 418 
 PHE   0.016   0.001   PHE J 285 
 HIS   0.002   0.001   HIS J 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 3809)
  covalent geometry    : angle       0.42243 ( 5126)
  hydrogen bonds       : bond        0.05205 (  121)
  hydrogen bonds       : angle       4.61228 (  351)

*********************** 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
  28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.206 
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: J  353 MET cc_start: 0.9734 (pmm) cc_final: 0.9437 (pmm)
REVERT: J  413 MET cc_start: 0.9026 (mmp) cc_final: 0.8778 (mmm)
REVERT: J  473 LEU cc_start: 0.9567 (tp) cc_final: 0.9313 (tt)
REVERT: J  483 MET cc_start: 0.9490 (mmp) cc_final: 0.9076 (mmm)
REVERT: J  508 MET cc_start: 0.9580 (mmp) cc_final: 0.9317 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1417
  time to fit residues: 5.1471
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  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.044081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.030340 restraints weight = 109600.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.031606 restraints weight = 58176.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.032453 restraints weight = 36576.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.033001 restraints weight = 26018.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.033403 restraints weight = 20554.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3809  Z= 0.161
  Angle     :  0.480   4.320   5126  Z= 0.265
  Chirality :  0.039   0.128    630
  Planarity :  0.003   0.028    663
  Dihedral  :  3.039  10.999    529
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  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: -0.93 (0.35), residues: 503
  helix:  0.15 (0.32), residues: 223
  sheet: -1.84 (0.67), residues: 54
  loop : -0.96 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG J 431 
 TYR   0.007   0.001   TYR J 124 
 PHE   0.012   0.002   PHE J 285 
 HIS   0.004   0.001   HIS J 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3809)
  covalent geometry    : angle       0.47970 ( 5126)
  hydrogen bonds       : bond        0.03739 (  121)
  hydrogen bonds       : angle       4.22883 (  351)

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.192 
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: J  353 MET cc_start: 0.9756 (pmm) cc_final: 0.9313 (pmm)
REVERT: J  413 MET cc_start: 0.9253 (mmp) cc_final: 0.8962 (mmm)
REVERT: J  508 MET cc_start: 0.9542 (mmp) cc_final: 0.9262 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1983
  time to fit residues: 6.3862
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  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0570
   chunk 34 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.5900

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.044335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.030681 restraints weight = 110160.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.031961 restraints weight = 57002.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.032839 restraints weight = 35517.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.033364 restraints weight = 25175.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.033762 restraints weight = 20021.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.4868

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= 0.084
  Angle     :  0.388   4.182   5126  Z= 0.211
  Chirality :  0.038   0.131    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.765   9.919    529
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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: -0.40 (0.37), residues: 503
  helix:  0.61 (0.33), residues: 223
  sheet: -1.48 (0.70), residues: 54
  loop : -0.74 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 308 
 TYR   0.005   0.001   TYR J 124 
 PHE   0.005   0.001   PHE J 355 
 HIS   0.002   0.000   HIS J  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 3809)
  covalent geometry    : angle       0.38776 ( 5126)
  hydrogen bonds       : bond        0.03353 (  121)
  hydrogen bonds       : angle       4.05556 (  351)

*********************** 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
  23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.215 
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  353 MET cc_start: 0.9740 (pmm) cc_final: 0.9316 (pmm)
REVERT: J  413 MET cc_start: 0.9221 (mmp) cc_final: 0.8918 (mmm)
REVERT: J  483 MET cc_start: 0.9479 (mmp) cc_final: 0.9047 (mmm)
REVERT: J  508 MET cc_start: 0.9509 (mmp) cc_final: 0.9215 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1751
  time to fit residues: 5.1563
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  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0050
   chunk 4 optimal weight:    0.0570
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0570
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.3230

-------------------------------------------------------------------------------
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 = 0.3291 r_free = 0.3291 target = 0.044641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.030839 restraints weight = 110482.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.032143 restraints weight = 57304.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.033010 restraints weight = 35672.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.033629 restraints weight = 25353.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.033945 restraints weight = 19950.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.019   3809  Z= 0.068
  Angle     :  0.366   4.035   5126  Z= 0.197
  Chirality :  0.038   0.125    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.626   9.981    529
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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: -0.03 (0.37), residues: 503
  helix:  0.85 (0.34), residues: 224
  sheet: -1.09 (0.73), residues: 54
  loop : -0.55 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 307 
 TYR   0.003   0.001   TYR J 124 
 PHE   0.005   0.001   PHE J 355 
 HIS   0.001   0.000   HIS J  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00148 ( 3809)
  covalent geometry    : angle       0.36642 ( 5126)
  hydrogen bonds       : bond        0.02973 (  121)
  hydrogen bonds       : angle       3.81857 (  351)

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.173 
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: J  353 MET cc_start: 0.9717 (pmm) cc_final: 0.9298 (pmm)
REVERT: J  413 MET cc_start: 0.9274 (mmp) cc_final: 0.8984 (mmm)
REVERT: J  483 MET cc_start: 0.9509 (mmp) cc_final: 0.9047 (mmm)
REVERT: J  508 MET cc_start: 0.9496 (mmp) cc_final: 0.9184 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1859
  time to fit residues: 5.9866
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  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7778

-------------------------------------------------------------------------------
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 = 0.3279 r_free = 0.3279 target = 0.044201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.030241 restraints weight = 112208.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.031536 restraints weight = 58808.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.032402 restraints weight = 36601.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.032970 restraints weight = 26054.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.033350 restraints weight = 20613.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.5357

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= 0.097
  Angle     :  0.390   4.564   5126  Z= 0.213
  Chirality :  0.038   0.125    630
  Planarity :  0.002   0.023    663
  Dihedral  :  2.681   9.468    529
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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:  0.30 (0.37), residues: 503
  helix:  1.08 (0.34), residues: 224
  sheet: -0.59 (0.84), residues: 45
  loop : -0.42 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 431 
 TYR   0.001   0.000   TYR J 297 
 PHE   0.004   0.001   PHE J 355 
 HIS   0.002   0.001   HIS J 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 3809)
  covalent geometry    : angle       0.38995 ( 5126)
  hydrogen bonds       : bond        0.02804 (  121)
  hydrogen bonds       : angle       3.81372 (  351)

*********************** 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
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  353 MET cc_start: 0.9732 (pmm) cc_final: 0.9477 (pmm)
REVERT: J  413 MET cc_start: 0.9269 (mmp) cc_final: 0.8989 (mmm)
REVERT: J  483 MET cc_start: 0.9501 (mmp) cc_final: 0.9072 (mmm)
REVERT: J  508 MET cc_start: 0.9469 (mmp) cc_final: 0.9152 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1828
  time to fit residues: 5.5476
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  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 41 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3256 r_free = 0.3256 target = 0.043459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.029892 restraints weight = 112916.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.031116 restraints weight = 59448.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.031940 restraints weight = 37257.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.032478 restraints weight = 26642.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.032784 restraints weight = 21148.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.5658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3809  Z= 0.110
  Angle     :  0.404   4.688   5126  Z= 0.223
  Chirality :  0.037   0.125    630
  Planarity :  0.002   0.023    663
  Dihedral  :  2.804   9.937    529
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  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:  0.44 (0.38), residues: 503
  helix:  1.13 (0.34), residues: 231
  sheet: -0.39 (0.86), residues: 45
  loop : -0.36 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 308 
 TYR   0.001   0.000   TYR J 297 
 PHE   0.004   0.001   PHE J 355 
 HIS   0.002   0.001   HIS J 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3809)
  covalent geometry    : angle       0.40372 ( 5126)
  hydrogen bonds       : bond        0.02762 (  121)
  hydrogen bonds       : angle       3.85680 (  351)

*********************** 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
  23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.237 
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: 0.9323 (tmm) cc_final: 0.9058 (tpp)
REVERT: J  353 MET cc_start: 0.9734 (pmm) cc_final: 0.9508 (pmm)
REVERT: J  413 MET cc_start: 0.9295 (mmp) cc_final: 0.9004 (mmm)
REVERT: J  483 MET cc_start: 0.9529 (mmp) cc_final: 0.9126 (mmm)
REVERT: J  508 MET cc_start: 0.9430 (mmp) cc_final: 0.9065 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2034
  time to fit residues: 5.8581
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  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.043500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.030219 restraints weight = 113958.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.031432 restraints weight = 59452.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.032248 restraints weight = 37202.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.032784 restraints weight = 26513.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.033118 restraints weight = 21083.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.5838

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= 0.085
  Angle     :  0.377   4.892   5126  Z= 0.205
  Chirality :  0.037   0.124    630
  Planarity :  0.002   0.021    663
  Dihedral  :  2.740   9.298    529
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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:  0.66 (0.38), residues: 503
  helix:  1.37 (0.34), residues: 231
  sheet: -0.20 (0.87), residues: 45
  loop : -0.33 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 307 
 TYR   0.002   0.000   TYR J 297 
 PHE   0.005   0.001   PHE J 355 
 HIS   0.001   0.000   HIS J 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 3809)
  covalent geometry    : angle       0.37734 ( 5126)
  hydrogen bonds       : bond        0.02510 (  121)
  hydrogen bonds       : angle       3.70125 (  351)

*********************** 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
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.225 
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: J   47 MET cc_start: 0.8508 (pmm) cc_final: 0.8237 (pmm)
REVERT: J  413 MET cc_start: 0.9335 (mmp) cc_final: 0.9023 (mmm)
REVERT: J  483 MET cc_start: 0.9573 (mmp) cc_final: 0.9160 (mmm)
REVERT: J  508 MET cc_start: 0.9403 (mmp) cc_final: 0.9045 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1740
  time to fit residues: 5.1860
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  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.3980
   chunk 26 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0040
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.043589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.030249 restraints weight = 113266.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.031468 restraints weight = 58617.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.032276 restraints weight = 36503.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.032777 restraints weight = 25962.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.033156 restraints weight = 20822.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.021   3809  Z= 0.069
  Angle     :  0.367   4.863   5126  Z= 0.198
  Chirality :  0.037   0.124    630
  Planarity :  0.002   0.022    663
  Dihedral  :  2.685   9.996    529
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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:  0.74 (0.38), residues: 503
  helix:  1.42 (0.34), residues: 231
  sheet: -0.14 (0.88), residues: 45
  loop : -0.27 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 307 
 TYR   0.002   0.000   TYR J 297 
 PHE   0.006   0.001   PHE J 355 
 HIS   0.001   0.000   HIS J 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00149 ( 3809)
  covalent geometry    : angle       0.36706 ( 5126)
  hydrogen bonds       : bond        0.02448 (  121)
  hydrogen bonds       : angle       3.62774 (  351)

********************** 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
  23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.224 
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: J   47 MET cc_start: 0.8454 (pmm) cc_final: 0.8149 (pmm)
REVERT: J  353 MET cc_start: 0.9750 (pmm) cc_final: 0.9372 (pmm)
REVERT: J  413 MET cc_start: 0.9305 (mmp) cc_final: 0.9007 (mmm)
REVERT: J  483 MET cc_start: 0.9600 (mmp) cc_final: 0.9177 (mmm)
REVERT: J  508 MET cc_start: 0.9387 (mmp) cc_final: 0.9031 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2141
  time to fit residues: 6.1403
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  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0050
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7194

-------------------------------------------------------------------------------
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 = 0.3257 r_free = 0.3257 target = 0.043233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.029824 restraints weight = 114678.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.031017 restraints weight = 60357.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.031789 restraints weight = 38024.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.032370 restraints weight = 27300.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.032681 restraints weight = 21638.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.6110

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= 0.089
  Angle     :  0.380   5.171   5126  Z= 0.207
  Chirality :  0.037   0.123    630
  Planarity :  0.002   0.021    663
  Dihedral  :  2.729   9.114    529
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  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:  1.46 (0.34), residues: 231
  sheet:  0.09 (0.89), residues: 45
  loop : -0.29 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 307 
 TYR   0.002   0.000   TYR J 297 
 PHE   0.005   0.001   PHE J 355 
 HIS   0.001   0.000   HIS J 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00179 ( 3809)
  covalent geometry    : angle       0.38043 ( 5126)
  hydrogen bonds       : bond        0.02383 (  121)
  hydrogen bonds       : angle       3.62794 (  351)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1813.48 seconds
wall clock time: 31 minutes 28.39 seconds (1888.39 seconds total)