Starting phenix.real_space_refine
on Wed Feb 12 11:24:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r9e_24324/02_2025/7r9e_24324.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r9e_24324/02_2025/7r9e_24324.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r9e_24324/02_2025/7r9e_24324.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r9e_24324/02_2025/7r9e_24324.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r9e_24324/02_2025/7r9e_24324.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r9e_24324/02_2025/7r9e_24324.cif"
  }
  resolution = 4.0
  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    3938      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 7726
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7726
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 3.97, per 1000 atoms: 0.51
  Number of scatterers: 7726
  At special positions: 0
  Unit cell: (91.8, 66.96, 111.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     O     759      8.00
     N     655      7.00
     C    2351      6.00
     H    3938      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.96
  Conformation dependent library (CDL) restraints added in 654.5 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:
      18 helices and 4 sheets defined
      52.5% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'J' and resid 20 through 37
      removed outlier: 3.605A  pdb=" N   THR J  34 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL J  35 " --> pdb=" O   ILE J  31 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   SER J  37 " --> pdb=" O   GLU J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 61 through 67
      removed outlier: 3.968A  pdb=" N   GLU J  67 " --> pdb=" O   THR J  63 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 74 through 89
      removed outlier: 4.134A  pdb=" N   LEU J  78 " --> pdb=" O   ALA J  74 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL J  81 " --> pdb=" O   MET J  77 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ALA J  82 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR J  84 " --> pdb=" O   GLU J  80 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN J  85 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU J  88 " --> pdb=" O   THR J  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 112
      removed outlier: 3.852A  pdb=" N   ALA J  96 " --> pdb=" O   GLY J  92 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL J  97 " --> pdb=" O   THR J  93 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL J  99 " --> pdb=" O   THR J  95 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU J 102 " --> pdb=" O   VAL J  98 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG J 105 " --> pdb=" O   GLY J 101 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA J 107 " --> pdb=" O   LEU J 103 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLU J 108 " --> pdb=" O   LEU J 104 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.534A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY J 123 " --> pdb=" O   ILE J 119 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR J 124 " --> pdb=" O   VAL J 120 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN J 129 " --> pdb=" O   GLN J 125 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN J 132 " --> pdb=" O   ALA J 128 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU J 134 " --> pdb=" O   LYS J 130 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LYS J 136 " --> pdb=" O   GLN J 132 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 146 through 162
      removed outlier: 4.120A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   MET J 155 " --> pdb=" O   THR J 151 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR J 156 " --> pdb=" O   LYS J 152 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER J 157 " --> pdb=" O   ILE J 153 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR J 159 " --> pdb=" O   MET J 155 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY J 160 " --> pdb=" O   THR J 156 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY J 162 " --> pdb=" O   ILE J 158 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 168 through 179
      removed outlier: 3.568A  pdb=" N   GLU J 172 " --> pdb=" O   GLU J 168 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE J 174 " --> pdb=" O   LEU J 170 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 189 through 191
      No H-bonds generated for 'chain 'J' and resid 189 through 191'
    Processing helix  chain 'J' and resid 260 through 280
      removed outlier: 3.975A  pdb=" N   GLU J 266 " --> pdb=" O   ILE J 262 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET J 268 " --> pdb=" O   GLN J 264 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LEU J 269 " --> pdb=" O   GLU J 265 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS J 270 " --> pdb=" O   GLU J 266 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASP J 271 " --> pdb=" O   LYS J 267 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET J 272 " --> pdb=" O   MET J 268 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 291 through 302
      removed outlier: 3.652A  pdb=" N   GLN J 295 " --> pdb=" O   ASP J 291 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA J 299 " --> pdb=" O   GLN J 295 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS J 300 " --> pdb=" O   HIS J 296 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 322
      removed outlier: 3.770A  pdb=" N   GLU J 315 " --> pdb=" O   LYS J 311 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LYS J 316 " --> pdb=" O   SER J 312 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU J 317 " --> pdb=" O   ASP J 313 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ALA J 318 " --> pdb=" O   MET J 314 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS J 319 " --> pdb=" O   GLU J 315 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 397
      removed outlier: 3.500A  pdb=" N   ILE J 377 " --> pdb=" O   THR J 373 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA J 383 " --> pdb=" O   GLU J 379 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ASP J 385 " --> pdb=" O   ALA J 381 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ASP J 386 " --> pdb=" O   ARG J 382 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL J 388 " --> pdb=" O   VAL J 384 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY J 389 " --> pdb=" O   ASP J 385 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   CYS J 393 " --> pdb=" O   GLY J 389 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   THR J 394 " --> pdb=" O   VAL J 390 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 407 through 420
      removed outlier: 3.720A  pdb=" N   LEU J 411 " --> pdb=" O   THR J 407 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS J 414 " --> pdb=" O   GLU J 410 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG J 416 " --> pdb=" O   SER J 412 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLU J 420 " --> pdb=" O   ARG J 416 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 426 through 437
      removed outlier: 3.620A  pdb=" N   VAL J 430 " --> pdb=" O   GLU J 426 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 438 through 449
      removed outlier: 3.729A  pdb=" N   ARG J 442 " --> pdb=" O   GLU J 438 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU J 444 " --> pdb=" O   ILE J 440 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA J 448 " --> pdb=" O   LEU J 444 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 451 through 463
      removed outlier: 4.471A  pdb=" N   VAL J 457 " --> pdb=" O   ILE J 453 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   LYS J 458 " --> pdb=" O   GLU J 454 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG J 460 " --> pdb=" O   LEU J 456 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA J 461 " --> pdb=" O   VAL J 457 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA J 462 " --> pdb=" O   LYS J 458 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   HIS J 463 " --> pdb=" O   VAL J 459 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 483 through 487
    Processing helix  chain 'J' and resid 492 through 511
      removed outlier: 3.552A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 4.287A  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: 3.666A  pdb=" N   VAL J 401 " --> pdb=" O   GLU J 490 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLU J 490 " --> pdb=" O   VAL J 401 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 193 through 195
      removed outlier: 3.543A  pdb=" N   MET J 367 " --> pdb=" O   LYS J 194 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 284 through 285
      removed outlier: 5.648A  pdb=" N   LEU J 284 " --> pdb=" O   ALA J 306 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'J' and resid 471 through 473

    121 hydrogen bonds defined for protein.
    360 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: 2.23

  Time building geometry restraints manager: 2.35 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3931
        1.03 -     1.23: 7
        1.23 -     1.42: 1405
        1.42 -     1.61: 2365
        1.61 -     1.81: 39
  Bond restraints: 7747
  Sorted by residual:
  bond pdb=" C   HIS J 361 "
       pdb=" N   PRO J 362 "
    ideal  model  delta    sigma   weight residual
    1.326  1.337 -0.010 1.44e-02 4.82e+03 5.23e-01
  bond pdb=" N   ILE J 455 "
       pdb=" CA  ILE J 455 "
    ideal  model  delta    sigma   weight residual
    1.452  1.460 -0.008 1.18e-02 7.18e+03 4.09e-01
  bond pdb=" C   GLU J 490 "
       pdb=" N   PRO J 491 "
    ideal  model  delta    sigma   weight residual
    1.331  1.338 -0.007 1.21e-02 6.83e+03 3.54e-01
  bond pdb=" CA  ALA J 364 "
       pdb=" C   ALA J 364 "
    ideal  model  delta    sigma   weight residual
    1.523  1.531 -0.007 1.34e-02 5.57e+03 3.09e-01
  bond pdb=" N   HIS J 361 "
       pdb=" CA  HIS J 361 "
    ideal  model  delta    sigma   weight residual
    1.457  1.464 -0.007 1.41e-02 5.03e+03 2.63e-01
  ... (remaining 7742 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.82: 12781
        0.82 -     1.64: 1311
        1.64 -     2.46: 38
        2.46 -     3.28: 9
        3.28 -     4.10: 6
  Bond angle restraints: 14145
  Sorted by residual:
  angle pdb=" N   ILE J 455 "
        pdb=" CA  ILE J 455 "
        pdb=" C   ILE J 455 "
      ideal   model   delta    sigma   weight residual
     112.96  109.50    3.46 1.00e+00 1.00e+00 1.20e+01
  angle pdb=" N   ILE J 440 "
        pdb=" CA  ILE J 440 "
        pdb=" C   ILE J 440 "
      ideal   model   delta    sigma   weight residual
     112.35  109.25    3.10 1.20e+00 6.94e-01 6.68e+00
  angle pdb=" N   ASN J 236 "
        pdb=" CA  ASN J 236 "
        pdb=" C   ASN J 236 "
      ideal   model   delta    sigma   weight residual
     114.62  112.10    2.52 1.14e+00 7.69e-01 4.88e+00
  angle pdb=" C   VAL J 439 "
        pdb=" N   ILE J 440 "
        pdb=" CA  ILE J 440 "
      ideal   model   delta    sigma   weight residual
     120.33  122.04   -1.71 8.00e-01 1.56e+00 4.54e+00
  angle pdb=" CA  ASN J 236 "
        pdb=" C   ASN J 236 "
        pdb=" N   CYS J 237 "
      ideal   model   delta    sigma   weight residual
     119.71  117.38    2.33 1.17e+00 7.31e-01 3.98e+00
  ... (remaining 14140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 3421
       17.35 -    34.71: 60
       34.71 -    52.06: 38
       52.06 -    69.42: 15
       69.42 -    86.77: 2
  Dihedral angle restraints: 3536
    sinusoidal: 2036
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  LYS J 300 "
           pdb=" CB  LYS J 300 "
           pdb=" CG  LYS J 300 "
           pdb=" CD  LYS J 300 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -97.60   37.60     3      1.50e+01 4.44e-03 6.58e+00
  dihedral pdb=" CA  ARG J  18 "
           pdb=" CB  ARG J  18 "
           pdb=" CG  ARG J  18 "
           pdb=" CD  ARG J  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -95.59   35.59     3      1.50e+01 4.44e-03 6.11e+00
  dihedral pdb=" CA  VAL J 304 "
           pdb=" CB  VAL J 304 "
           pdb=" CG2 VAL J 304 "
           pdb="HG23 VAL J 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
     240.00  153.23   86.77     2      3.00e+01 1.11e-03 5.32e+00
  ... (remaining 3533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 374
       0.024 -    0.047: 155
       0.047 -    0.071: 48
       0.071 -    0.095: 25
       0.095 -    0.118: 28
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  VAL J 227 "
            pdb=" N   VAL J 227 "
            pdb=" C   VAL J 227 "
            pdb=" CB  VAL J 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  ILE J 369 "
            pdb=" N   ILE J 369 "
            pdb=" C   ILE J 369 "
            pdb=" CB  ILE J 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  chirality pdb=" CA  ILE J 290 "
            pdb=" N   ILE J 290 "
            pdb=" C   ILE J 290 "
            pdb=" CB  ILE J 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.40e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS J 361 "    0.010 5.00e-02 4.00e+02   1.51e-02 3.66e-01
        pdb=" N   PRO J 362 "   -0.026 5.00e-02 4.00e+02
        pdb=" CA  PRO J 362 "    0.008 5.00e-02 4.00e+02
        pdb=" CD  PRO J 362 "    0.008 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   1.33e-02 2.82e-01
        pdb=" N   PRO J 117 "   -0.023 5.00e-02 4.00e+02
        pdb=" CA  PRO J 117 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO J 117 "    0.007 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.008 5.00e-02 4.00e+02   1.28e-02 2.62e-01
        pdb=" N   PRO J 255 "    0.022 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO J 255 "   -0.007 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.28: 1093
        2.28 -     2.86: 18245
        2.86 -     3.44: 17610
        3.44 -     4.02: 22505
        4.02 -     4.60: 35020
  Nonbonded interactions: 94473
  Sorted by model distance:
  nonbonded pdb=" O   ASP J 482 "
            pdb="HD21 ASN J 486 "
     model   vdw
     1.705 2.450
  nonbonded pdb=" OE1 GLU J 240 "
            pdb=" H   GLU J 240 "
     model   vdw
     1.710 2.450
  nonbonded pdb=" O   CYS J 470 "
            pdb=" H   MET J 483 "
     model   vdw
     1.736 2.450
  nonbonded pdb=" O   VAL J 409 "
            pdb=" HG  SER J 412 "
     model   vdw
     1.742 2.450
  nonbonded pdb=" O   SER J 199 "
            pdb=" HE  ARG J 370 "
     model   vdw
     1.745 2.450
  ... (remaining 94468 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:             1.250
  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:             0.150
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.480
  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:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
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   0.013   3809  Z= 0.100
  Angle     :  0.375   4.097   5126  Z= 0.235
  Chirality :  0.037   0.118    630
  Planarity :  0.001   0.015    663
  Dihedral  :  4.449  37.604   1463
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  1.39 %
    Allowed  :  9.94 %
    Favored  : 88.67 %
  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: -3.58 (0.34), residues: 503
  helix: -3.22 (0.26), residues: 179
  sheet: -3.44 (0.83), residues: 33
  loop : -1.64 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 296 
 PHE   0.003   0.001   PHE J 285 
 TYR   0.001   0.000   TYR J 418 
 ARG   0.002   0.000   ARG J 346 

*********************** 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
  47 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  367 MET cc_start: 0.8076 (mmm) cc_final: 0.7826 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.3319
  time to fit residues: 19.7252
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  : 0.556 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
J  72 HIS
J 236 ASN
J 500 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.077085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.050870 restraints weight = 73518.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.052395 restraints weight = 34605.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.053375 restraints weight = 20928.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2314

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= 0.194
  Angle     :  0.552   5.428   5126  Z= 0.307
  Chirality :  0.039   0.126    630
  Planarity :  0.003   0.030    663
  Dihedral  :  2.740  18.578    529
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.36 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.90 %
    Favored  : 93.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.24 (0.33), residues: 503
  helix: -1.83 (0.30), residues: 219
  sheet: -2.77 (1.00), residues: 26
  loop : -2.37 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 375 
 PHE   0.008   0.002   PHE J 355 
 TYR   0.004   0.001   TYR J 418 
 ARG   0.002   0.000   ARG J  29 

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

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  268 MET cc_start: 0.8432 (tmm) cc_final: 0.8097 (ppp)
REVERT: J  367 MET cc_start: 0.8117 (mmm) cc_final: 0.7906 (tpp)
  outliers start: 3
  outliers final: 1
  residues processed: 28
  average time/residue: 0.3184
  time to fit residues: 11.9474
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.074135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.047794 restraints weight = 75745.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.049274 restraints weight = 36131.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.050197 restraints weight = 22094.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3809  Z= 0.235
  Angle     :  0.529   4.937   5126  Z= 0.292
  Chirality :  0.039   0.118    630
  Planarity :  0.004   0.065    663
  Dihedral  :  3.308  15.505    529
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  5.41 %
    Favored  : 93.61 %
  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: -2.14 (0.36), residues: 503
  helix: -0.69 (0.33), residues: 240
  sheet: -2.77 (0.98), residues: 26
  loop : -2.00 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J 116 
 PHE   0.013   0.002   PHE J 355 
 TYR   0.003   0.001   TYR J 124 
 ARG   0.003   0.000   ARG J  29 

*********************** 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: 4
    poor density    : 24
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  108 GLU cc_start: 0.9034 (mp0) cc_final: 0.8724 (pm20)
  outliers start: 4
  outliers final: 3
  residues processed: 27
  average time/residue: 0.3092
  time to fit residues: 11.3316
Evaluate side-chains
  27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue  375 HIS
Chi-restraints excluded: chain J residue  510 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.074360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.047232 restraints weight = 76699.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.048769 restraints weight = 35966.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.049750 restraints weight = 21945.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3809  Z= 0.170
  Angle     :  0.476   6.276   5126  Z= 0.252
  Chirality :  0.038   0.115    630
  Planarity :  0.003   0.028    663
  Dihedral  :  3.135  15.398    529
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  5.65 %
    Favored  : 93.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.70 (0.37), residues: 503
  helix: -0.24 (0.34), residues: 245
  sheet: -2.47 (0.98), residues: 26
  loop : -1.92 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 116 
 PHE   0.009   0.001   PHE J 355 
 TYR   0.002   0.001   TYR J 297 
 ARG   0.001   0.000   ARG J  29 

*********************** 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
  28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  367 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7564 (tpp)
  outliers start: 4
  outliers final: 2
  residues processed: 26
  average time/residue: 0.3604
  time to fit residues: 12.2198
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue  367 MET
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.073206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.047146 restraints weight = 73249.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.048682 restraints weight = 33514.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.049625 restraints weight = 20113.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3809  Z= 0.196
  Angle     :  0.491   5.409   5126  Z= 0.265
  Chirality :  0.038   0.122    630
  Planarity :  0.003   0.030    663
  Dihedral  :  3.165  14.396    529
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.39 %
    Favored  : 92.63 %
  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: -1.32 (0.38), residues: 503
  helix:  0.05 (0.34), residues: 241
  sheet: -2.09 (1.04), residues: 26
  loop : -1.71 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J 116 
 PHE   0.009   0.001   PHE J 355 
 TYR   0.003   0.001   TYR J 418 
 ARG   0.002   0.000   ARG J 370 

*********************** 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
  28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.2594
  time to fit residues: 9.5897
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue   72 HIS
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.073837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.047080 restraints weight = 74958.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.048505 restraints weight = 34522.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.049353 restraints weight = 21008.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3809  Z= 0.135
  Angle     :  0.456   5.151   5126  Z= 0.238
  Chirality :  0.038   0.121    630
  Planarity :  0.003   0.028    663
  Dihedral  :  3.075  13.920    529
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.39 %
    Favored  : 92.63 %
  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: -0.91 (0.38), residues: 503
  helix:  0.38 (0.34), residues: 240
  sheet: -1.76 (1.07), residues: 26
  loop : -1.49 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.008   0.001   PHE J 355 
 TYR   0.002   0.000   TYR J 297 
 ARG   0.001   0.000   ARG J 399 

*********************** 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
  28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 26
  average time/residue: 0.2582
  time to fit residues: 9.4078
Evaluate side-chains
  27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue   72 HIS
Chi-restraints excluded: chain J residue  367 MET
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 45 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.073470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.047348 restraints weight = 73638.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.048823 restraints weight = 34309.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.049662 restraints weight = 20895.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.4689

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= 0.143
  Angle     :  0.468   5.999   5126  Z= 0.246
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.027    663
  Dihedral  :  3.018  13.828    529
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.63 %
    Favored  : 92.38 %
  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: -0.68 (0.38), residues: 503
  helix:  0.56 (0.34), residues: 240
  sheet: -1.59 (1.10), residues: 26
  loop : -1.37 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J 116 
 PHE   0.006   0.001   PHE J 355 
 TYR   0.002   0.000   TYR J 297 
 ARG   0.001   0.000   ARG J 346 

*********************** 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
  27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 25
  average time/residue: 0.2743
  time to fit residues: 9.5905
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue  367 MET
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   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 = 0.3860 r_free = 0.3860 target = 0.073750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.046900 restraints weight = 76322.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.048327 restraints weight = 34756.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.049164 restraints weight = 21043.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.4867

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= 0.134
  Angle     :  0.460   6.379   5126  Z= 0.239
  Chirality :  0.038   0.122    630
  Planarity :  0.002   0.027    663
  Dihedral  :  3.008  13.403    529
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.88 %
    Favored  : 92.38 %
  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: -0.54 (0.39), residues: 503
  helix:  0.74 (0.34), residues: 240
  sheet: -1.47 (1.11), residues: 26
  loop : -1.38 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   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 346 

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 24
  average time/residue: 0.2690
  time to fit residues: 9.2171
Evaluate side-chains
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.072033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.045410 restraints weight = 75621.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.046914 restraints weight = 34439.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.047829 restraints weight = 20580.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3809  Z= 0.237
  Angle     :  0.532   8.097   5126  Z= 0.286
  Chirality :  0.038   0.127    630
  Planarity :  0.003   0.029    663
  Dihedral  :  3.217  13.598    529
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.63 %
    Favored  : 92.63 %
  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: -0.68 (0.38), residues: 503
  helix:  0.60 (0.33), residues: 243
  sheet: -1.48 (1.12), residues: 26
  loop : -1.45 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS J 116 
 PHE   0.007   0.001   PHE J 355 
 TYR   0.003   0.001   TYR J 418 
 ARG   0.002   0.000   ARG J 399 

*********************** 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
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 23
  average time/residue: 0.2626
  time to fit residues: 8.5637
Evaluate side-chains
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue  367 MET
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0670
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 33 optimal weight:    0.0370
   overall best weight:    0.3596

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.073771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.047044 restraints weight = 74169.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.048557 restraints weight = 34578.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.049454 restraints weight = 20968.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.5340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3809  Z= 0.129
  Angle     :  0.487   8.036   5126  Z= 0.246
  Chirality :  0.039   0.127    630
  Planarity :  0.002   0.027    663
  Dihedral  :  3.089  12.895    529
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.13 %
    Favored  : 92.38 %
  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: -0.23 (0.39), residues: 503
  helix:  0.96 (0.35), residues: 241
  sheet: -1.27 (1.13), residues: 26
  loop : -1.19 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J  72 
 PHE   0.007   0.001   PHE J 433 
 TYR   0.003   0.001   TYR J 418 
 ARG   0.002   0.000   ARG J 346 

********************** 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
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 23
  average time/residue: 0.2823
  time to fit residues: 9.1421
Evaluate side-chains
  22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  367 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.073761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.047086 restraints weight = 73637.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.048556 restraints weight = 34501.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.049477 restraints weight = 21051.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3809  Z= 0.133
  Angle     :  0.484   7.522   5126  Z= 0.248
  Chirality :  0.038   0.133    630
  Planarity :  0.002   0.027    663
  Dihedral  :  3.008  13.300    529
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.37 %
    Favored  : 92.38 %
  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: -0.09 (0.39), residues: 503
  helix:  1.07 (0.35), residues: 242
  sheet: -1.14 (1.14), residues: 26
  loop : -1.14 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J 116 
 PHE   0.005   0.001   PHE J 355 
 TYR   0.001   0.000   TYR J 297 
 ARG   0.003   0.000   ARG J 346 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3375.35 seconds
wall clock time: 60 minutes 2.03 seconds (3602.03 seconds total)