Starting phenix.real_space_refine
on Wed Feb 12 11:45:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r9m_24329/02_2025/7r9m_24329.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r9m_24329/02_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_24329/02_2025/7r9m_24329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r9m_24329/02_2025/7r9m_24329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r9m_24329/02_2025/7r9m_24329.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r9m_24329/02_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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7727
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7727
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 4.15, per 1000 atoms: 0.54
  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: 1.78
  Conformation dependent library (CDL) restraints added in 679.3 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: 0.54
  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: 2.56

  Time building geometry restraints manager: 2.18 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:             1.060
  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:             0.140
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.520
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.210
-------------------------------------------------------------------------------
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  : 0.612 
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: 0.3491
  time to fit residues: 18.9978
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  : 0.585 
-------------------------------------------------------------------------------
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 = 52)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.061597 restraints weight = 61463.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.063029 restraints weight = 27896.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.063809 restraints weight = 17576.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9470 (mtp) cc_final: 0.8754 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.3338
  time to fit residues: 11.4211
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  : 0.575 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0170
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.092851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.063826 restraints weight = 62620.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.065440 restraints weight = 25885.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.066278 restraints weight = 15526.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3293

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= 0.157
  Angle     :  0.447   4.005   5126  Z= 0.242
  Chirality :  0.039   0.125    630
  Planarity :  0.003   0.027    663
  Dihedral  :  2.490  12.520    529
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  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: -2.30 (0.34), residues: 503
  helix: -0.81 (0.32), residues: 224
  sheet: -2.46 (0.70), residues: 46
  loop : -1.99 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J 296 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.007   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
  27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9434 (mtp) cc_final: 0.8752 (tpp)
  outliers start: 4
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3368
  time to fit residues: 11.2878
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  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.092329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.063980 restraints weight = 60082.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.065612 restraints weight = 24806.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.066603 restraints weight = 14703.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3809  Z= 0.144
  Angle     :  0.439   5.169   5126  Z= 0.234
  Chirality :  0.039   0.128    630
  Planarity :  0.003   0.027    663
  Dihedral  :  2.571  16.045    529
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  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: -1.70 (0.35), residues: 503
  helix: -0.23 (0.33), residues: 225
  sheet: -2.66 (0.79), residues: 32
  loop : -1.76 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 296 
 PHE   0.004   0.001   PHE J 433 
 TYR   0.007   0.001   TYR J 124 
 ARG   0.002   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  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   39 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9030 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3491
  time to fit residues: 11.6079
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  : 0.570 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0670
   chunk 34 optimal weight:    0.0070
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.092414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.063975 restraints weight = 59911.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.065597 restraints weight = 24517.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.066455 restraints weight = 14479.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3990

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= 0.114
  Angle     :  0.401   4.945   5126  Z= 0.210
  Chirality :  0.039   0.125    630
  Planarity :  0.002   0.027    663
  Dihedral  :  2.428  15.799    529
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  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: -1.43 (0.35), residues: 503
  helix:  0.08 (0.33), residues: 228
  sheet: -2.31 (0.83), residues: 32
  loop : -1.76 (0.36), residues: 243

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  22 

*********************** 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
  26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   39 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.9000 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3645
  time to fit residues: 12.3731
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  : 0.640 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 49 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.091990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063468 restraints weight = 60324.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.065089 restraints weight = 24630.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.066084 restraints weight = 14570.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3809  Z= 0.135
  Angle     :  0.418   5.604   5126  Z= 0.219
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.027    663
  Dihedral  :  2.471  15.006    529
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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: -0.98 (0.35), residues: 503
  helix:  0.51 (0.33), residues: 219
  sheet: -2.12 (0.86), 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   0.002   0.000   ARG J  22 

*********************** 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  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   39 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9002 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3619
  time to fit residues: 12.0642
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  : 0.615 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 20 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0570
   chunk 25 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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 = 0.092022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.063646 restraints weight = 60174.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.065313 restraints weight = 24280.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.066196 restraints weight = 14265.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3809  Z= 0.110
  Angle     :  0.389   5.216   5126  Z= 0.204
  Chirality :  0.038   0.125    630
  Planarity :  0.002   0.027    663
  Dihedral  :  2.420  14.447    529
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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: -0.77 (0.36), residues: 503
  helix:  0.74 (0.34), residues: 219
  sheet: -1.96 (0.88), residues: 32
  loop : -1.46 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 463 
 PHE   0.003   0.000   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.001   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  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  367 MET cc_start: 0.8370 (mtt) cc_final: 0.7626 (ppp)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3480
  time to fit residues: 11.5004
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  : 0.584 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.090138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.060063 restraints weight = 61379.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.061441 restraints weight = 26051.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.062125 restraints weight = 16076.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3809  Z= 0.184
  Angle     :  0.432   5.719   5126  Z= 0.233
  Chirality :  0.039   0.124    630
  Planarity :  0.003   0.026    663
  Dihedral  :  2.601  14.256    529
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.16 %
    Favored  : 94.59 %
  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: -0.69 (0.36), residues: 503
  helix:  0.80 (0.34), residues: 222
  sheet: -1.99 (0.88), residues: 32
  loop : -1.42 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.009   0.001   TYR J 124 
 ARG   0.002   0.000   ARG J 105 

*********************** 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
  24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  367 MET cc_start: 0.8412 (mtt) cc_final: 0.7695 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 24
  average time/residue: 0.3320
  time to fit residues: 10.6309
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  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0070
   chunk 33 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.7402

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.090216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.060645 restraints weight = 60026.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.062101 restraints weight = 24986.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.062974 restraints weight = 15113.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3809  Z= 0.130
  Angle     :  0.407   5.676   5126  Z= 0.214
  Chirality :  0.039   0.130    630
  Planarity :  0.002   0.025    663
  Dihedral  :  2.559  14.340    529
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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: -0.51 (0.36), residues: 503
  helix:  0.98 (0.34), residues: 227
  sheet: -1.95 (0.88), residues: 32
  loop : -1.41 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS J 463 
 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 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: 2
    poor density    : 23
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9421 (mtp) cc_final: 0.8902 (tpp)
REVERT: J  367 MET cc_start: 0.8357 (mtt) cc_final: 0.7693 (ppp)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3231
  time to fit residues: 10.6850
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  : 0.584 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   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 = 0.4027 r_free = 0.4027 target = 0.090357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.060927 restraints weight = 60147.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.062356 restraints weight = 25253.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.063104 restraints weight = 15479.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3809  Z= 0.133
  Angle     :  0.412   5.886   5126  Z= 0.215
  Chirality :  0.038   0.123    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.555  14.054    529
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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: -0.47 (0.36), residues: 503
  helix:  1.04 (0.34), residues: 228
  sheet: -1.95 (0.88), residues: 32
  loop : -1.42 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.006   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
  25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9421 (mtp) cc_final: 0.8906 (tpp)
REVERT: J  367 MET cc_start: 0.8420 (mtt) cc_final: 0.7724 (ppp)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3273
  time to fit residues: 11.0253
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  : 0.571 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0470
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 16 optimal weight:    0.1980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.4278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.091265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.061060 restraints weight = 59779.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.062587 restraints weight = 24395.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.063455 restraints weight = 14655.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3809  Z= 0.106
  Angle     :  0.394   5.922   5126  Z= 0.204
  Chirality :  0.039   0.127    630
  Planarity :  0.002   0.024    663
  Dihedral  :  2.515  13.809    529
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.41 %
    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: -0.39 (0.36), residues: 503
  helix:  1.14 (0.34), residues: 228
  sheet: -2.01 (0.86), residues: 32
  loop : -1.40 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 463 
 PHE   0.004   0.000   PHE J 355 
 TYR   0.004   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J 399 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3349.57 seconds
wall clock time: 59 minutes 36.61 seconds (3576.61 seconds total)