Starting phenix.real_space_refine
on Wed Feb 12 10:14:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r9u_24331/02_2025/7r9u_24331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r9u_24331/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r9u_24331/02_2025/7r9u_24331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r9u_24331/02_2025/7r9u_24331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r9u_24331/02_2025/7r9u_24331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r9u_24331/02_2025/7r9u_24331.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.32, per 1000 atoms: 0.56
  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: 1.81
  Conformation dependent library (CDL) restraints added in 687.8 milliseconds
  

  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: 0.55
  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: 2.46

  Time building geometry restraints manager: 2.21 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:             0.920
  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:             0.120
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.150
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.590
-------------------------------------------------------------------------------
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= 0.100
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.002   0.000   HIS J  72 
 PHE   0.001   0.000   PHE J 355 
 TYR   0.001   0.000   TYR J 418 
 ARG   0.001   0.000   ARG J 522 

*********************** 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  : 0.655 
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: 0.3737
  time to fit residues: 25.8644
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  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.9184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.046532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.032726 restraints weight = 112342.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.034044 restraints weight = 58806.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.034972 restraints weight = 36819.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3809  Z= 0.181
  Angle     :  0.508   4.839   5126  Z= 0.282
  Chirality :  0.039   0.132    630
  Planarity :  0.003   0.048    663
  Dihedral  :  2.803  10.604    529
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.98 %
    Favored  : 95.83 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.34), residues: 503
  helix: -1.79 (0.30), residues: 217
  sheet: -2.81 (0.53), residues: 68
  loop : -1.53 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J 375 
 PHE   0.013   0.002   PHE J 355 
 TYR   0.015   0.003   TYR J 124 
 ARG   0.002   0.000   ARG J 431 

*********************** 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
  36 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.709 
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: 0.9717 (pmm) cc_final: 0.9458 (pmm)
REVERT: J  413 MET cc_start: 0.9028 (mmp) cc_final: 0.8769 (mmm)
REVERT: J  473 LEU cc_start: 0.9556 (tp) cc_final: 0.9282 (tt)
REVERT: J  483 MET cc_start: 0.9498 (mmp) cc_final: 0.9067 (mmm)
REVERT: J  508 MET cc_start: 0.9630 (mmp) cc_final: 0.9312 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.3889
  time to fit residues: 17.8438
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  : 0.629 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.0050
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7596

-------------------------------------------------------------------------------
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 = 0.3329 r_free = 0.3329 target = 0.046122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.032196 restraints weight = 108603.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.033476 restraints weight = 57601.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.034367 restraints weight = 36290.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3717

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= 0.132
  Angle     :  0.411   4.328   5126  Z= 0.226
  Chirality :  0.038   0.129    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.638  10.075    529
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.36), residues: 503
  helix: -0.68 (0.33), residues: 218
  sheet: -2.45 (0.55), residues: 70
  loop : -1.20 (0.43), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 116 
 PHE   0.012   0.001   PHE J 285 
 TYR   0.004   0.001   TYR J 418 
 ARG   0.002   0.000   ARG J 307 

*********************** 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
  27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.657 
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: 0.9733 (pmm) cc_final: 0.9356 (pmm)
REVERT: J  413 MET cc_start: 0.9135 (mmp) cc_final: 0.8882 (mmm)
REVERT: J  473 LEU cc_start: 0.9583 (tp) cc_final: 0.9341 (tt)
REVERT: J  483 MET cc_start: 0.9520 (mmp) cc_final: 0.9105 (mmm)
REVERT: J  508 MET cc_start: 0.9583 (mmp) cc_final: 0.9289 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.4324
  time to fit residues: 14.7207
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  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.044941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.030969 restraints weight = 110741.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.032234 restraints weight = 59696.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.033095 restraints weight = 37978.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.4376

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= 0.155
  Angle     :  0.425   4.293   5126  Z= 0.234
  Chirality :  0.038   0.127    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.800  10.886    529
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.63
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.36), residues: 503
  helix:  0.23 (0.33), residues: 218
  sheet: -1.39 (0.69), residues: 55
  loop : -0.96 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 116 
 PHE   0.018   0.002   PHE J 285 
 TYR   0.006   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 382 

*********************** 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
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.575 
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  285 PHE cc_start: 0.9590 (m-10) cc_final: 0.9131 (m-80)
REVERT: J  353 MET cc_start: 0.9765 (pmm) cc_final: 0.9314 (pmm)
REVERT: J  413 MET cc_start: 0.9263 (mmp) cc_final: 0.8977 (mmm)
REVERT: J  508 MET cc_start: 0.9554 (mmp) cc_final: 0.9249 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.4746
  time to fit residues: 14.8755
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  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.044882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.030840 restraints weight = 109794.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.032090 restraints weight = 57841.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.032934 restraints weight = 36339.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.4875

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= 0.144
  Angle     :  0.419   4.277   5126  Z= 0.230
  Chirality :  0.038   0.136    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.773  10.318    529
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.37), residues: 503
  helix:  0.72 (0.34), residues: 217
  sheet: -1.03 (0.73), residues: 55
  loop : -0.74 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J  72 
 PHE   0.007   0.001   PHE J 285 
 TYR   0.002   0.001   TYR J 297 
 ARG   0.001   0.000   ARG J 382 

*********************** 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  : 0.675 
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: 0.9762 (pmm) cc_final: 0.9345 (pmm)
REVERT: J  413 MET cc_start: 0.9336 (mmp) cc_final: 0.9020 (mmm)
REVERT: J  483 MET cc_start: 0.9497 (mmp) cc_final: 0.9030 (mmm)
REVERT: J  508 MET cc_start: 0.9541 (mmp) cc_final: 0.9211 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.4000
  time to fit residues: 11.3659
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  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3302 r_free = 0.3302 target = 0.044913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.030938 restraints weight = 110014.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.032197 restraints weight = 57314.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.033060 restraints weight = 35932.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.5103

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= 0.115
  Angle     :  0.384   4.089   5126  Z= 0.208
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.732  10.170    529
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.37), residues: 503
  helix:  0.97 (0.35), residues: 218
  sheet: -0.80 (0.82), residues: 45
  loop : -0.59 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 375 
 PHE   0.012   0.001   PHE J 285 
 TYR   0.001   0.000   TYR J 297 
 ARG   0.001   0.000   ARG J 307 

*********************** 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
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.598 
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: 0.9732 (pmm) cc_final: 0.9471 (pmm)
REVERT: J  413 MET cc_start: 0.9367 (mmp) cc_final: 0.9056 (mmm)
REVERT: J  483 MET cc_start: 0.9526 (mmp) cc_final: 0.9118 (mmm)
REVERT: J  508 MET cc_start: 0.9511 (mmp) cc_final: 0.9169 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.3684
  time to fit residues: 11.4905
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  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0270
   chunk 20 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3294 r_free = 0.3294 target = 0.044659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.030614 restraints weight = 110650.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.031909 restraints weight = 57087.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.032792 restraints weight = 35584.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.5310

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= 0.110
  Angle     :  0.380   4.438   5126  Z= 0.206
  Chirality :  0.038   0.126    630
  Planarity :  0.002   0.023    663
  Dihedral  :  2.705   9.486    529
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.53
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.38), residues: 503
  helix:  1.18 (0.35), residues: 218
  sheet: -0.52 (0.84), residues: 45
  loop : -0.45 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.009   0.001   PHE J 285 
 TYR   0.001   0.000   TYR J 297 
 ARG   0.001   0.000   ARG J 307 

*********************** 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
  23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.641 
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: 0.9723 (pmm) cc_final: 0.9460 (pmm)
REVERT: J  413 MET cc_start: 0.9303 (mmp) cc_final: 0.9023 (mmm)
REVERT: J  483 MET cc_start: 0.9466 (mmp) cc_final: 0.9091 (mmm)
REVERT: J  508 MET cc_start: 0.9468 (mmp) cc_final: 0.9141 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.3822
  time to fit residues: 11.5273
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  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3259 r_free = 0.3259 target = 0.043327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.029621 restraints weight = 111135.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.030841 restraints weight = 58221.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.031675 restraints weight = 36348.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.5755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3809  Z= 0.175
  Angle     :  0.440   4.670   5126  Z= 0.244
  Chirality :  0.038   0.127    630
  Planarity :  0.003   0.027    663
  Dihedral  :  2.977  11.149    529
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.38), residues: 503
  helix:  1.10 (0.34), residues: 223
  sheet: -0.47 (0.77), residues: 55
  loop : -0.41 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 116 
 PHE   0.009   0.001   PHE J 285 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.002   0.000   ARG J 431 

*********************** 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
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.576 
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   47 MET cc_start: 0.8481 (pmm) cc_final: 0.8184 (pmm)
REVERT: J  155 MET cc_start: 0.9370 (tmm) cc_final: 0.9079 (tpp)
REVERT: J  353 MET cc_start: 0.9739 (pmm) cc_final: 0.9509 (pmm)
REVERT: J  413 MET cc_start: 0.9375 (mmp) cc_final: 0.9056 (mmm)
REVERT: J  483 MET cc_start: 0.9479 (mmp) cc_final: 0.9110 (mmm)
REVERT: J  508 MET cc_start: 0.9459 (mmp) cc_final: 0.9081 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.3901
  time to fit residues: 11.1849
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  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    1.0186

-------------------------------------------------------------------------------
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 = 0.3267 r_free = 0.3267 target = 0.043486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.029821 restraints weight = 114862.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.031042 restraints weight = 59381.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.031877 restraints weight = 37064.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.5916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3809  Z= 0.136
  Angle     :  0.412   4.658   5126  Z= 0.227
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.025    663
  Dihedral  :  2.898  10.635    529
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.38), residues: 503
  helix:  1.27 (0.34), residues: 223
  sheet: -0.09 (0.88), residues: 45
  loop : -0.43 (0.40), residues: 235

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

*********************** 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
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.696 
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   47 MET cc_start: 0.8451 (pmm) cc_final: 0.8095 (pmm)
REVERT: J  353 MET cc_start: 0.9749 (pmm) cc_final: 0.9533 (pmm)
REVERT: J  413 MET cc_start: 0.9353 (mmp) cc_final: 0.9032 (mmm)
REVERT: J  483 MET cc_start: 0.9507 (mmp) cc_final: 0.9162 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.4745
  time to fit residues: 13.5451
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  : 0.672 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.043410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.029867 restraints weight = 112588.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.031067 restraints weight = 58601.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.031883 restraints weight = 36694.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.6010

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= 0.113
  Angle     :  0.393   4.830   5126  Z= 0.212
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.023    663
  Dihedral  :  2.846  10.136    529
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.38), residues: 503
  helix:  1.34 (0.34), residues: 225
  sheet:  0.07 (0.89), residues: 45
  loop : -0.37 (0.41), residues: 233

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

********************** 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
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.494 
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   47 MET cc_start: 0.8436 (pmm) cc_final: 0.8043 (pmm)
REVERT: J  413 MET cc_start: 0.9375 (mmp) cc_final: 0.9063 (mmm)
REVERT: J  483 MET cc_start: 0.9532 (mmp) cc_final: 0.9166 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.3756
  time to fit residues: 10.7864
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  : 0.538 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 48 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0050
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.3994

-------------------------------------------------------------------------------
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 = 0.3280 r_free = 0.3280 target = 0.043916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.030190 restraints weight = 111622.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.031423 restraints weight = 58182.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.032222 restraints weight = 36311.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.6044

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= 0.098
  Angle     :  0.379   4.850   5126  Z= 0.203
  Chirality :  0.038   0.126    630
  Planarity :  0.002   0.022    663
  Dihedral  :  2.755   8.526    529
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.92
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.38), residues: 503
  helix:  1.49 (0.35), residues: 224
  sheet:  0.21 (0.92), residues: 45
  loop : -0.32 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.006   0.001   PHE J 355 
 TYR   0.002   0.000   TYR J 297 
 ARG   0.002   0.000   ARG J 307 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3128.78 seconds
wall clock time: 55 minutes 54.53 seconds (3354.53 seconds total)