Starting phenix.real_space_refine
on Mon Mar 11 08:12:05 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/03_2024/7r9m_24329.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/03_2024/7r9m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/03_2024/7r9m_24329.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/03_2024/7r9m_24329.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/03_2024/7r9m_24329.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/03_2024/7r9m_24329.pdb"
  }
  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
    Residue "J ARG  382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "J PHE  433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J ARG  522": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.82, per 1000 atoms: 0.49
  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  - 3.50
        Amino acid           : False - 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: 5.69
  Conformation dependent library (CDL) restraints added in 774.0 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: 0.61
  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: 2.35

  Time building geometry restraints manager: 5.83 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:
      100.89 -   106.96: 58
      106.96 -   113.04: 9878
      113.04 -   119.11: 1585
      119.11 -   125.19: 2574
      125.19 -   131.26: 52
  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 1.850
  nonbonded pdb=" OE1 GLU J 245 "
            pdb=" H   GLU J 245 "
     model   vdw
     1.656 1.850
  nonbonded pdb=" OE1 GLU J 168 "
            pdb=" H   GLU J 168 "
     model   vdw
     1.679 1.850
  nonbonded pdb=" OE1 GLU J 263 "
            pdb=" H   GLU J 263 "
     model   vdw
     1.696 1.850
  nonbonded pdb=" OE1 GLU J  33 "
            pdb=" HE  ARG J  36 "
     model   vdw
     1.701 1.850
  ... (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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.110
  Extract box with map and model:          4.660
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     26.990
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.690
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.640 
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: 0.3508
  time to fit residues: 19.1637
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:   40.0000
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
J 296 HIS
J 447 ASN
J 474 ASN
J 500 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3809  Z= 0.268
  Angle     :  0.565   3.902   5126  Z= 0.318
  Chirality :  0.041   0.134    630
  Planarity :  0.004   0.023    663
  Dihedral  :  2.417  10.553    529
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.16 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.91 %
    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: -3.63 (0.31), residues: 503
  helix: -2.31 (0.27), residues: 222
  sheet: -2.72 (0.68), residues: 46
  loop : -2.33 (0.35), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 296 
 PHE   0.005   0.001   PHE J 433 
 TYR   0.015   0.003   TYR J 124 
 ARG   0.004   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
  28 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9487 (mtp) cc_final: 0.8832 (tpp)
REVERT: J  504 GLU cc_start: 0.9334 (tt0) cc_final: 0.9038 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 27
  average time/residue: 0.3457
  time to fit residues: 12.3958
Evaluate side-chains
  27 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   39 LEU
Chi-restraints excluded: chain J residue  223 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3809  Z= 0.219
  Angle     :  0.495   4.943   5126  Z= 0.268
  Chirality :  0.039   0.129    630
  Planarity :  0.003   0.031    663
  Dihedral  :  2.694  13.577    529
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.39 %
    Favored  : 92.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.34), residues: 503
  helix: -0.82 (0.32), residues: 224
  sheet: -2.32 (0.70), residues: 46
  loop : -1.94 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 463 
 PHE   0.005   0.001   PHE J 476 
 TYR   0.010   0.002   TYR J 124 
 ARG   0.006   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
  28 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9456 (mtp) cc_final: 0.8720 (tpp)
REVERT: J  504 GLU cc_start: 0.9361 (tt0) cc_final: 0.9110 (tm-30)
REVERT: J  508 MET cc_start: 0.9300 (mtp) cc_final: 0.9086 (ttm)
  outliers start: 4
  outliers final: 2
  residues processed: 27
  average time/residue: 0.3191
  time to fit residues: 11.6694
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  191 ASP
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 34 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0050
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.5994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3807

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= 0.120
  Angle     :  0.414   4.842   5126  Z= 0.218
  Chirality :  0.038   0.126    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.488  15.453    529
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.14 %
    Favored  : 93.12 %
  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: -1.48 (0.35), residues: 503
  helix: -0.21 (0.33), residues: 224
  sheet: -2.04 (0.72), residues: 46
  loop : -1.46 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 375 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.006   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
  28 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9447 (mtp) cc_final: 0.8739 (tpp)
REVERT: J  504 GLU cc_start: 0.9333 (tt0) cc_final: 0.9107 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 27
  average time/residue: 0.3181
  time to fit residues: 11.4786
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 19 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 43 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3809  Z= 0.122
  Angle     :  0.413   5.058   5126  Z= 0.215
  Chirality :  0.038   0.125    630
  Planarity :  0.002   0.025    663
  Dihedral  :  2.429  14.380    529
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.39 %
    Favored  : 93.12 %
  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: -1.17 (0.36), residues: 503
  helix:  0.09 (0.33), residues: 227
  sheet: -1.74 (0.74), residues: 46
  loop : -1.41 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 375 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.002   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 fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  504 GLU cc_start: 0.9357 (tt0) cc_final: 0.9133 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3328
  time to fit residues: 11.2981
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 11 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0570
   chunk 4 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0030
   chunk 25 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0000
   chunk 27 optimal weight:   10.0000
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.2112

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.4147

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= 0.097
  Angle     :  0.394   4.769   5126  Z= 0.202
  Chirality :  0.038   0.125    630
  Planarity :  0.002   0.025    663
  Dihedral  :  2.353  13.310    529
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.63 %
    Favored  : 92.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.37), residues: 503
  helix:  0.60 (0.35), residues: 218
  sheet: -1.40 (0.77), residues: 46
  loop : -1.23 (0.39), residues: 239

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   0.003   0.001   TYR J 124 
 ARG   0.001   0.000   ARG J  36 

*********************** 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 fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  504 GLU cc_start: 0.9346 (tt0) cc_final: 0.9086 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3289
  time to fit residues: 11.0147
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4650

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= 0.223
  Angle     :  0.472   5.134   5126  Z= 0.259
  Chirality :  0.039   0.126    630
  Planarity :  0.003   0.032    663
  Dihedral  :  2.687  15.172    529
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.39 %
    Favored  : 93.12 %
  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: -0.89 (0.36), residues: 503
  helix:  0.37 (0.33), residues: 229
  sheet: -1.26 (0.76), residues: 46
  loop : -1.40 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS J 463 
 PHE   0.004   0.001   PHE J 355 
 TYR   0.011   0.002   TYR J 124 
 ARG   0.003   0.000   ARG J 105 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  504 GLU cc_start: 0.9394 (tt0) cc_final: 0.9145 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 26
  average time/residue: 0.3402
  time to fit residues: 11.7138
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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 23 optimal weight:    3.9990
   chunk 4 optimal weight:    0.1980
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 44 optimal weight:    0.5980
   chunk 27 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4785

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= 0.112
  Angle     :  0.416   5.707   5126  Z= 0.214
  Chirality :  0.039   0.132    630
  Planarity :  0.002   0.026    663
  Dihedral  :  2.533  13.946    529
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.63 %
    Favored  : 92.87 %
  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: -0.37 (0.37), residues: 503
  helix:  0.88 (0.34), residues: 222
  sheet: -1.10 (0.76), residues: 46
  loop : -1.16 (0.39), residues: 235

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   0.006   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
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  504 GLU cc_start: 0.9355 (tt0) cc_final: 0.9113 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3251
  time to fit residues: 10.8878
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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 40 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4897

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= 0.116
  Angle     :  0.410   5.650   5126  Z= 0.211
  Chirality :  0.038   0.127    630
  Planarity :  0.002   0.025    663
  Dihedral  :  2.468  14.041    529
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.63 %
    Favored  : 92.87 %
  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: -0.22 (0.37), residues: 503
  helix:  1.01 (0.34), residues: 225
  sheet: -0.99 (0.78), residues: 46
  loop : -1.12 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 375 
 PHE   0.003   0.000   PHE J 355 
 TYR   0.005   0.001   TYR J 124 
 ARG   0.001   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
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9455 (mtp) cc_final: 0.8888 (tpp)
REVERT: J  504 GLU cc_start: 0.9368 (tt0) cc_final: 0.9130 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3732
  time to fit residues: 13.0316
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.5102

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= 0.157
  Angle     :  0.436   5.721   5126  Z= 0.229
  Chirality :  0.038   0.123    630
  Planarity :  0.002   0.028    663
  Dihedral  :  2.596  14.666    529
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.88 %
    Favored  : 92.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.37), residues: 503
  helix:  0.92 (0.34), residues: 229
  sheet: -0.96 (0.79), residues: 46
  loop : -1.18 (0.39), residues: 228

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   0.007   0.001   TYR J 124 
 ARG   0.002   0.000   ARG J 105 

********************** 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
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  155 MET cc_start: 0.9451 (mtp) cc_final: 0.8890 (tpp)
REVERT: J  504 GLU cc_start: 0.9378 (tt0) cc_final: 0.9150 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.3343
  time to fit residues: 11.1708
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  104 LEU
Chi-restraints excluded: chain J residue  375 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0070
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.7002

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.091807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.063293 restraints weight = 60448.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.064839 restraints weight = 25458.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.065767 restraints weight = 15370.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5246

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= 0.124
  Angle     :  0.412   5.717   5126  Z= 0.213
  Chirality :  0.039   0.125    630
  Planarity :  0.002   0.023    663
  Dihedral  :  2.534  13.645    529
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.88 %
    Favored  : 92.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.37), residues: 503
  helix:  1.09 (0.34), residues: 229
  sheet: -0.87 (0.79), residues: 46
  loop : -1.13 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   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  22 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2342.52 seconds
wall clock time: 41 minutes 59.69 seconds (2519.69 seconds total)