Starting phenix.real_space_refine
on Wed Mar 12 12:10:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r9m_24329/03_2025/7r9m_24329.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r9m_24329/03_2025/7r9m_24329.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/7r9m_24329/03_2025/7r9m_24329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r9m_24329/03_2025/7r9m_24329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r9m_24329/03_2025/7r9m_24329.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r9m_24329/03_2025/7r9m_24329.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    3939      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.52, per 1000 atoms: 0.58
  Number of scatterers: 7727
  At special positions: 0
  Unit cell: (82.08, 74.52, 103.68, 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: 2.10
  Conformation dependent library (CDL) restraints added in 813.0 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
      53.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'J' and resid 20 through 34
      removed outlier: 3.557A  pdb=" N   ASN J  24 " --> pdb=" O   ALA J  20 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE J  25 " --> pdb=" O   GLN J  21 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG J  29 " --> pdb=" O   ILE J  25 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE J  30 " --> pdb=" O   LEU J  26 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE J  31 " --> pdb=" O   ALA J  27 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA J  32 " --> pdb=" O   GLY J  28 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU J  33 " --> pdb=" O   ARG J  29 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   THR J  34 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 61 through 68
      removed outlier: 3.604A  pdb=" N   ARG J  66 " --> pdb=" O   VAL J  62 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLU J  67 " --> pdb=" O   THR J  63 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 72 through 74
      No H-bonds generated for 'chain 'J' and resid 72 through 74'
    Processing helix  chain 'J' and resid 75 through 89
      removed outlier: 3.851A  pdb=" N   ILE J  79 " --> pdb=" O   ALA J  75 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL J  81 " --> pdb=" O   MET J  77 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA J  82 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR J  84 " --> pdb=" O   GLU J  80 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN J  85 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLU J  86 " --> pdb=" O   ALA J  82 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 112
      removed outlier: 3.513A  pdb=" N   VAL J  97 " --> pdb=" O   THR J  93 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL J  99 " --> pdb=" O   THR J  95 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU J 102 " --> pdb=" O   VAL J  98 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU J 103 " --> pdb=" O   VAL J  99 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLU J 108 " --> pdb=" O   LEU J 104 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU J 110 " --> pdb=" O   LYS J 106 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.829A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLY J 123 " --> pdb=" O   ILE J 119 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU J 134 " --> pdb=" O   LYS J 130 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LYS J 136 " --> pdb=" O   GLN J 132 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 147 through 159
      removed outlier: 3.694A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE J 153 " --> pdb=" O   ILE J 149 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   MET J 155 " --> pdb=" O   THR J 151 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   THR J 159 " --> pdb=" O   MET J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 160 through 162
      No H-bonds generated for 'chain 'J' and resid 160 through 162'
    Processing helix  chain 'J' and resid 166 through 180
      removed outlier: 3.709A  pdb=" N   GLU J 172 " --> pdb=" O   GLU J 168 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL J 175 " --> pdb=" O   ALA J 171 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLU J 176 " --> pdb=" O   GLU J 172 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER J 179 " --> pdb=" O   VAL J 175 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 202 through 206
      removed outlier: 3.588A  pdb=" N   ASP J 205 " --> pdb=" O   SER J 202 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 279
      removed outlier: 4.468A  pdb=" N   GLU J 260 " --> pdb=" O   ALA J 256 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE J 262 " --> pdb=" O   LEU J 258 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLU J 263 " --> pdb=" O   MET J 259 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS J 267 " --> pdb=" O   GLU J 263 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET J 268 " --> pdb=" O   GLN J 264 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE J 276 " --> pdb=" O   MET J 272 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER J 279 " --> pdb=" O   GLU J 275 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 293 through 300
      removed outlier: 3.735A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 312 through 321
      removed outlier: 3.892A  pdb=" N   LYS J 316 " --> pdb=" O   SER J 312 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA J 318 " --> pdb=" O   MET J 314 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS J 319 " --> pdb=" O   GLU J 315 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 398
      removed outlier: 3.627A  pdb=" N   ILE J 377 " --> pdb=" O   THR J 373 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU J 378 " --> pdb=" O   GLU J 374 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLU J 379 " --> pdb=" O   HIS J 375 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL J 380 " --> pdb=" O   VAL J 376 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA J 383 " --> pdb=" O   GLU J 379 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP J 385 " --> pdb=" O   ALA J 381 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ASP J 386 " --> pdb=" O   ARG J 382 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY J 389 " --> pdb=" O   ASP J 385 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR J 394 " --> pdb=" O   VAL J 390 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE J 395 " --> pdb=" O   VAL J 391 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLU J 396 " --> pdb=" O   GLY J 392 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 405 through 420
      removed outlier: 3.868A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ARG J 416 " --> pdb=" O   SER J 412 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLU J 420 " --> pdb=" O   ARG J 416 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 426 through 437
      removed outlier: 3.653A  pdb=" N   VAL J 430 " --> pdb=" O   GLU J 426 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA J 432 " --> pdb=" O   LEU J 428 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU J 437 " --> pdb=" O   PHE J 433 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 439 through 449
      removed outlier: 3.589A  pdb=" N   LEU J 444 " --> pdb=" O   ILE J 440 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA J 445 " --> pdb=" O   PRO J 441 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 451 through 463
      removed outlier: 3.840A  pdb=" N   VAL J 457 " --> pdb=" O   ILE J 453 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LYS J 458 " --> pdb=" O   GLU J 454 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ARG J 460 " --> pdb=" O   LEU J 456 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA J 461 " --> pdb=" O   VAL J 457 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA J 462 " --> pdb=" O   LYS J 458 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS J 463 " --> pdb=" O   VAL J 459 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 482 through 487
      removed outlier: 3.578A  pdb=" N   ASN J 486 " --> pdb=" O   ASP J 482 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 492 through 511
      removed outlier: 4.156A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 4.084A  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: 3.590A  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 197
      removed outlier: 6.897A  pdb=" N   LYS J 194 " --> pdb=" O   MET J 367 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   ILE J 369 " --> pdb=" O   LYS J 194 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   GLU J 196 " --> pdb=" O   ILE J 369 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU J 368 " --> pdb=" O   GLU J 207 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLU J 207 " --> pdb=" O   LEU J 368 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 213 through 214
      removed outlier: 4.026A  pdb=" N   VAL J 214 " --> pdb=" O   ILE J 354 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE J 354 " --> pdb=" O   VAL J 214 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL J 343 " --> pdb=" O   VAL J 227 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL J 227 " --> pdb=" O   VAL J 343 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 281 through 283
      removed outlier: 8.012A  pdb=" N   LYS J 231 " --> pdb=" O   ASN J 282 " (cutoff:3.500A)

    123 hydrogen bonds defined for protein.
    357 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: 2.52

  Time building geometry restraints manager: 2.57 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=" CA  ALA J 248 "
       pdb=" C   ALA J 248 "
    ideal  model  delta    sigma   weight residual
    1.529  1.522  0.007 1.04e-02 9.25e+03 4.87e-01
  bond pdb=" N   GLU J  71 "
       pdb=" CA  GLU J  71 "
    ideal  model  delta    sigma   weight residual
    1.468  1.460  0.008 1.24e-02 6.50e+03 4.68e-01
  bond pdb=" N   ILE J 455 "
       pdb=" CA  ILE J 455 "
    ideal  model  delta    sigma   weight residual
    1.452  1.459 -0.007 1.18e-02 7.18e+03 3.44e-01
  bond pdb=" CA  ILE J 193 "
       pdb=" CB  ILE J 193 "
    ideal  model  delta    sigma   weight residual
    1.540  1.532  0.008 1.36e-02 5.41e+03 3.24e-01
  bond pdb=" C   VAL J 212 "
       pdb=" O   VAL J 212 "
    ideal  model  delta    sigma   weight residual
    1.236  1.230  0.007 1.19e-02 7.06e+03 3.16e-01
  ... (remaining 7743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.78: 12647
        0.78 -     1.55: 1438
        1.55 -     2.33: 44
        2.33 -     3.10: 11
        3.10 -     3.88: 7
  Bond angle restraints: 14147
  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  109.58    3.38 1.00e+00 1.00e+00 1.14e+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  109.29    3.06 1.20e+00 6.94e-01 6.50e+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  122.13   -1.80 8.00e-01 1.56e+00 5.04e+00
  angle pdb=" N   GLN J 145 "
        pdb=" CA  GLN J 145 "
        pdb=" C   GLN J 145 "
      ideal   model   delta    sigma   weight residual
     114.12  111.13    2.99 1.39e+00 5.18e-01 4.64e+00
  angle pdb=" C   ILE J 440 "
        pdb=" CA  ILE J 440 "
        pdb=" CB  ILE J 440 "
      ideal   model   delta    sigma   weight residual
     114.00  111.38    2.62 1.31e+00 5.83e-01 3.99e+00
  ... (remaining 14142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.82: 3348
       11.82 -    23.63: 108
       23.63 -    35.45: 38
       35.45 -    47.26: 22
       47.26 -    59.08: 21
  Dihedral angle restraints: 3537
    sinusoidal: 2036
      harmonic: 1501
  Sorted by residual:
  dihedral pdb=" CB  MET J 259 "
           pdb=" CG  MET J 259 "
           pdb=" SD  MET J 259 "
           pdb=" CE  MET J 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -90.97   30.97     3      1.50e+01 4.44e-03 4.98e+00
  dihedral pdb=" N   LEU J  26 "
           pdb=" CA  LEU J  26 "
           pdb=" CB  LEU J  26 "
           pdb=" CG  LEU J  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -90.40   30.40     3      1.50e+01 4.44e-03 4.84e+00
  dihedral pdb=" CB  MET J 272 "
           pdb=" CG  MET J 272 "
           pdb=" SD  MET J 272 "
           pdb=" CE  MET J 272 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -89.94   29.94     3      1.50e+01 4.44e-03 4.73e+00
  ... (remaining 3534 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 395
       0.025 -    0.050: 141
       0.050 -    0.074: 42
       0.074 -    0.099: 25
       0.099 -    0.124: 27
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ILE J 303 "
            pdb=" N   ILE J 303 "
            pdb=" C   ILE J 303 "
            pdb=" CB  ILE J 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE J 193 "
            pdb=" N   ILE J 193 "
            pdb=" C   ILE J 193 "
            pdb=" CB  ILE J 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-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    2.56   -0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.010 5.00e-02 4.00e+02   1.53e-02 3.76e-01
        pdb=" N   PRO J 255 "    0.026 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.008 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   GLY J  40 "    0.007 5.00e-02 4.00e+02   1.12e-02 2.01e-01
        pdb=" N   PRO J  41 "   -0.019 5.00e-02 4.00e+02
        pdb=" CA  PRO J  41 "    0.006 5.00e-02 4.00e+02
        pdb=" CD  PRO J  41 "    0.006 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS J 116 "    0.007 5.00e-02 4.00e+02   1.05e-02 1.77e-01
        pdb=" N   PRO J 117 "   -0.018 5.00e-02 4.00e+02
        pdb=" CA  PRO J 117 "    0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J 117 "    0.006 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 535
        2.24 -     2.83: 17868
        2.83 -     3.42: 17908
        3.42 -     4.01: 23056
        4.01 -     4.60: 36280
  Nonbonded interactions: 95647
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU J 148 "
            pdb=" H   GLU J 148 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" OE1 GLU J 245 "
            pdb=" H   GLU J 245 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" OE1 GLU J 168 "
            pdb=" H   GLU J 168 "
     model   vdw
     1.679 2.450
  nonbonded pdb=" OE1 GLU J 263 "
            pdb=" H   GLU J 263 "
     model   vdw
     1.696 2.450
  nonbonded pdb=" OE1 GLU J  33 "
            pdb=" HE  ARG J  36 "
     model   vdw
     1.701 2.450
  ... (remaining 95642 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:             64.780
  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:             0.130
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.490
  Find NCS groups from input model:        0.060
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   89.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
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= 0.103
  Angle     :  0.380   3.877   5126  Z= 0.234
  Chirality :  0.038   0.124    630
  Planarity :  0.001   0.015    663
  Dihedral  :  4.685  38.566   1463
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  8.35 %
    Favored  : 90.85 %
  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: -4.83 (0.28), residues: 503
  helix: -3.89 (0.21), residues: 196
  sheet: -3.74 (0.49), residues: 55
  loop : -2.39 (0.33), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 361 
 PHE   0.001   0.000   PHE J 285 
 TYR   0.002   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
  43 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  114 ASN cc_start: 0.8773 (m-40) cc_final: 0.8550 (t0)
REVERT: J  155 MET cc_start: 0.9443 (mtp) cc_final: 0.8664 (tpp)
REVERT: J  504 GLU cc_start: 0.9322 (tt0) cc_final: 0.9092 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.3645
  time to fit residues: 19.9553
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
J 447 ASN
J 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.092545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.061662 restraints weight = 61463.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.063058 restraints weight = 27770.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.063771 restraints weight = 17499.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3809  Z= 0.273
  Angle     :  0.586   4.426   5126  Z= 0.328
  Chirality :  0.042   0.131    630
  Planarity :  0.003   0.025    663
  Dihedral  :  2.735  11.543    529
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.67 %
    Favored  : 95.09 %
  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: -3.40 (0.32), residues: 503
  helix: -2.02 (0.28), residues: 219
  sheet: -2.72 (0.69), residues: 46
  loop : -2.31 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 296 
 PHE   0.009   0.001   PHE J 433 
 TYR   0.016   0.003   TYR J 124 
 ARG   0.003   0.000   ARG J  22 

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9470 (mtp) cc_final: 0.8752 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.4556
  time to fit residues: 15.9233
Evaluate side-chains
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
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:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 24 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
J 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.094609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.062281 restraints weight = 61642.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.063962 restraints weight = 27429.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.064843 restraints weight = 17016.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3315

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= 0.157
  Angle     :  0.446   3.712   5126  Z= 0.242
  Chirality :  0.039   0.125    630
  Planarity :  0.003   0.028    663
  Dihedral  :  2.498  12.806    529
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.65 %
    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: -2.28 (0.34), residues: 503
  helix: -0.80 (0.32), residues: 224
  sheet: -2.45 (0.70), residues: 46
  loop : -1.98 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J 296 
 PHE   0.005   0.001   PHE J 355 
 TYR   0.008   0.001   TYR J 124 
 ARG   0.002   0.000   ARG J  22 

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9429 (mtp) cc_final: 0.8742 (tpp)
REVERT: J  508 MET cc_start: 0.8890 (mtp) cc_final: 0.8688 (ttm)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3416
  time to fit residues: 11.5220
Evaluate side-chains
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
Chi-restraints excluded: chain J residue  104 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.092401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.061399 restraints weight = 61576.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.062989 restraints weight = 26727.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.063916 restraints weight = 16414.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3961

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= 0.182
  Angle     :  0.475   5.286   5126  Z= 0.254
  Chirality :  0.039   0.130    630
  Planarity :  0.003   0.027    663
  Dihedral  :  2.687  15.304    529
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.65 %
    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: -1.68 (0.35), residues: 503
  helix: -0.23 (0.32), residues: 225
  sheet: -2.56 (0.82), residues: 32
  loop : -1.75 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 463 
 PHE   0.006   0.001   PHE J 433 
 TYR   0.010   0.002   TYR J 124 
 ARG   0.004   0.000   ARG J  22 

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

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   39 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9024 (tt)
REVERT: J  508 MET cc_start: 0.8849 (mtp) cc_final: 0.8646 (ttm)
  outliers start: 3
  outliers final: 1
  residues processed: 26
  average time/residue: 0.3575
  time to fit residues: 12.3023
Evaluate side-chains
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
Chi-restraints excluded: chain J residue  191 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5256

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.091962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.063751 restraints weight = 60245.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.065319 restraints weight = 24988.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.066162 restraints weight = 14995.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3809  Z= 0.111
  Angle     :  0.391   4.373   5126  Z= 0.206
  Chirality :  0.039   0.133    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.460  15.087    529
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.41 %
    Favored  : 93.86 %
  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: -1.38 (0.35), residues: 503
  helix:  0.11 (0.33), residues: 228
  sheet: -2.26 (0.86), residues: 32
  loop : -1.72 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 463 
 PHE   0.003   0.001   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 442 

*********************** 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
  27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   39 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9018 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.3116
  time to fit residues: 10.8767
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  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
Chi-restraints excluded: chain J residue  104 LEU
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 0 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0470
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6880

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.090872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063473 restraints weight = 60642.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.065093 restraints weight = 24997.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.065953 restraints weight = 14703.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3809  Z= 0.133
  Angle     :  0.403   5.037   5126  Z= 0.214
  Chirality :  0.039   0.125    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.483  14.647    529
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.16 %
    Favored  : 94.10 %
  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: -0.92 (0.36), residues: 503
  helix:  0.59 (0.34), residues: 219
  sheet: -2.01 (0.89), residues: 32
  loop : -1.52 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 296 
 PHE   0.003   0.001   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 105 

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

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   39 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9036 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3205
  time to fit residues: 10.7939
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  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
Chi-restraints excluded: chain J residue  104 LEU
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 14 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 20 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.090937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.061126 restraints weight = 59444.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.062618 restraints weight = 24500.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.063488 restraints weight = 14889.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3809  Z= 0.138
  Angle     :  0.410   4.907   5126  Z= 0.218
  Chirality :  0.039   0.125    630
  Planarity :  0.002   0.027    663
  Dihedral  :  2.538  13.935    529
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  4.91 %
    Favored  : 94.35 %
  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: -0.82 (0.36), residues: 503
  helix:  0.74 (0.34), residues: 225
  sheet: -2.15 (0.76), residues: 42
  loop : -1.51 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 296 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.007   0.001   TYR J 124 
 ARG   0.003   0.000   ARG J  22 

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  367 MET cc_start: 0.8283 (mtt) cc_final: 0.7746 (ppp)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.4153
  time to fit residues: 14.3620
Evaluate side-chains
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
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 38 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.090669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.060705 restraints weight = 59390.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.062206 restraints weight = 23900.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.062986 restraints weight = 14446.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4768

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= 0.130
  Angle     :  0.403   5.956   5126  Z= 0.212
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.025    663
  Dihedral  :  2.534  13.965    529
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.16 %
    Favored  : 94.35 %
  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: -0.50 (0.37), residues: 503
  helix:  0.99 (0.34), residues: 227
  sheet: -1.93 (0.89), residues: 32
  loop : -1.40 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 296 
 PHE   0.004   0.000   PHE J 355 
 TYR   0.006   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 399 

*********************** 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
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9419 (mtp) cc_final: 0.8903 (tpp)
REVERT: J  367 MET cc_start: 0.8314 (mtt) cc_final: 0.7751 (ppp)
  outliers start: 2
  outliers final: 2
  residues processed: 24
  average time/residue: 0.3184
  time to fit residues: 10.2087
Evaluate side-chains
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
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 35 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.089476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.059083 restraints weight = 61805.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.060484 restraints weight = 24993.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.061158 restraints weight = 15235.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3809  Z= 0.176
  Angle     :  0.438   5.645   5126  Z= 0.234
  Chirality :  0.039   0.124    630
  Planarity :  0.003   0.027    663
  Dihedral  :  2.650  13.614    529
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.41 %
    Favored  : 94.10 %
  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: -0.52 (0.36), residues: 503
  helix:  0.98 (0.34), residues: 228
  sheet: -1.97 (0.90), residues: 32
  loop : -1.43 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J  72 
 PHE   0.005   0.001   PHE J 355 
 TYR   0.007   0.001   TYR J 124 
 ARG   0.002   0.000   ARG J 105 

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

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9418 (mtp) cc_final: 0.8909 (tpp)
REVERT: J  367 MET cc_start: 0.8384 (mtt) cc_final: 0.7756 (ppp)
  outliers start: 2
  outliers final: 2
  residues processed: 24
  average time/residue: 0.3508
  time to fit residues: 11.2899
Evaluate side-chains
  23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
Chi-restraints excluded: chain J residue  191 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0870
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 4 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.090198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.060612 restraints weight = 59901.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.062102 restraints weight = 24962.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.062925 restraints weight = 15114.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5137

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     :  0.419   6.098   5126  Z= 0.215
  Chirality :  0.039   0.128    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.588  13.828    529
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.90 %
    Favored  : 93.86 %
  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: -0.39 (0.37), residues: 503
  helix:  1.11 (0.34), residues: 228
  sheet: -1.86 (0.89), residues: 32
  loop : -1.39 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J  72 
 PHE   0.004   0.000   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 399 

********************** 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: 1
    poor density    : 23
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9418 (mtp) cc_final: 0.8904 (tpp)
REVERT: J  367 MET cc_start: 0.8334 (mtt) cc_final: 0.7755 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 24
  average time/residue: 0.3340
  time to fit residues: 10.8940
Evaluate side-chains
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0970
   chunk 42 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5356

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.090204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.060736 restraints weight = 60304.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.062196 restraints weight = 25013.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.063076 restraints weight = 15187.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.5202

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= 0.117
  Angle     :  0.408   6.060   5126  Z= 0.211
  Chirality :  0.039   0.127    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.565  13.335    529
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.90 %
    Favored  : 93.86 %
  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: -0.35 (0.36), residues: 503
  helix:  1.14 (0.34), residues: 228
  sheet: -1.70 (0.74), residues: 46
  loop : -1.34 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.004   0.000   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 442 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3871.41 seconds
wall clock time: 68 minutes 6.89 seconds (4086.89 seconds total)