Starting phenix.real_space_refine
on Mon Mar 11 08:10:05 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/03_2024/7r9k_24328.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/03_2024/7r9k_24328.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/03_2024/7r9k_24328.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/03_2024/7r9k_24328.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/03_2024/7r9k_24328.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/03_2024/7r9k_24328.pdb"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2351      2.51       5
     N     655      2.21       5
     O     759      1.98       5
     H    3938      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    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: 7726
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7726
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 3.99, per 1000 atoms: 0.52
  Number of scatterers: 7726
  At special positions: 0
  Unit cell: (75.6, 77.76, 104.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     O     759      8.00
     N     655      7.00
     C    2351      6.00
     H    3938      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 5.76
  Conformation dependent library (CDL) restraints added in 856.5 milliseconds
  

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  938

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 4 sheets defined
      54.3% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'J' and resid 20 through 35
      removed outlier: 3.862A  pdb=" N   LEU J  26 " --> pdb=" O   ARG J  22 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY J  28 " --> pdb=" O   ASN J  24 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE J  31 " --> pdb=" O   ALA J  27 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL J  35 " --> pdb=" O   ILE J  31 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 61 through 66
    Processing helix  chain 'J' and resid 75 through 89
      removed outlier: 3.896A  pdb=" N   ILE J  79 " --> pdb=" O   ALA J  75 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL J  81 " --> pdb=" O   MET J  77 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA J  82 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS J  87 " --> pdb=" O   LYS J  83 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU J  88 " --> pdb=" O   THR J  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 113
      removed outlier: 3.842A  pdb=" N   ALA J  96 " --> pdb=" O   GLY J  92 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL J  97 " --> pdb=" O   THR J  93 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA J 100 " --> pdb=" O   ALA J  96 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU J 103 " --> pdb=" O   VAL J  99 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN J 113 " --> pdb=" O   GLU J 109 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.795A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL J 121 " --> pdb=" O   PRO J 117 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS J 122 " --> pdb=" O   THR J 118 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS J 136 " --> pdb=" O   GLN J 132 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE J 138 " --> pdb=" O   LEU J 134 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 148 through 162
      removed outlier: 3.960A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET J 155 " --> pdb=" O   THR J 151 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR J 156 " --> pdb=" O   LYS J 152 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER J 157 " --> pdb=" O   ILE J 153 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LYS J 161 " --> pdb=" O   SER J 157 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY J 162 " --> pdb=" O   ILE J 158 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 167 through 182
      removed outlier: 4.097A  pdb=" N   GLU J 172 " --> pdb=" O   GLU J 168 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA J 180 " --> pdb=" O   GLU J 176 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL J 181 " --> pdb=" O   ALA J 177 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL J 182 " --> pdb=" O   VAL J 178 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 202 through 206
      removed outlier: 3.543A  pdb=" N   ASP J 205 " --> pdb=" O   SER J 202 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 271
      removed outlier: 3.799A  pdb=" N   GLU J 260 " --> pdb=" O   ALA J 256 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE J 261 " --> pdb=" O   LYS J 257 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   ILE J 262 " --> pdb=" O   LEU J 258 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 271 through 279
      removed outlier: 3.691A  pdb=" N   GLU J 275 " --> pdb=" O   ASP J 271 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   SER J 279 " --> pdb=" O   GLU J 275 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 291 through 302
      removed outlier: 3.989A  pdb=" N   HIS J 296 " --> pdb=" O   ASP J 292 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 322
      removed outlier: 3.723A  pdb=" N   MET J 314 " --> pdb=" O   LYS J 310 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU J 315 " --> pdb=" O   LYS J 311 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA J 318 " --> pdb=" O   MET J 314 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 398
      removed outlier: 4.552A  pdb=" N   GLU J 379 " --> pdb=" O   HIS J 375 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL J 380 " --> pdb=" O   VAL J 376 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ARG J 382 " --> pdb=" O   GLU J 378 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA J 383 " --> pdb=" O   GLU J 379 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP J 385 " --> pdb=" O   ALA J 381 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL J 388 " --> pdb=" O   VAL J 384 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY J 389 " --> pdb=" O   ASP J 385 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR J 394 " --> pdb=" O   VAL J 390 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 405 through 422
      removed outlier: 3.836A  pdb=" N   GLU J 410 " --> pdb=" O   SER J 406 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU J 411 " --> pdb=" O   THR J 407 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER J 412 " --> pdb=" O   GLU J 408 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG J 416 " --> pdb=" O   SER J 412 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TYR J 418 " --> pdb=" O   LYS J 414 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLY J 421 " --> pdb=" O   GLU J 417 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE J 422 " --> pdb=" O   TYR J 418 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 425 through 438
      removed outlier: 3.806A  pdb=" N   ALA J 429 " --> pdb=" O   ARG J 425 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 439 through 447
      removed outlier: 3.559A  pdb=" N   THR J 443 " --> pdb=" O   VAL J 439 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA J 445 " --> pdb=" O   PRO J 441 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 453 through 463
      removed outlier: 3.605A  pdb=" N   VAL J 457 " --> pdb=" O   ILE J 453 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LYS J 458 " --> pdb=" O   GLU J 454 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 482 through 487
      removed outlier: 3.974A  pdb=" N   ASN J 486 " --> pdb=" O   ASP J 482 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY J 487 " --> pdb=" O   MET J 483 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 482 through 487'
    Processing helix  chain 'J' and resid 492 through 512
      removed outlier: 3.693A  pdb=" N   GLN J 497 " --> pdb=" O   ARG J 493 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU J 504 " --> pdb=" O   GLN J 500 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU J 509 " --> pdb=" O   SER J 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 49
      removed outlier: 4.251A  pdb=" N   LYS J  46 " --> pdb=" O   THR J  58 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   THR J  58 " --> pdb=" O   LYS J  46 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL J  56 " --> pdb=" O   LEU J  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 140 through 141
    Processing sheet with id=AA3, first strand: chain 'J' and resid 193 through 197
      removed outlier: 7.115A  pdb=" N   LYS J 194 " --> pdb=" O   MET J 367 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   ILE J 369 " --> pdb=" O   LYS J 194 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLU J 196 " --> pdb=" O   ILE J 369 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU J 368 " --> pdb=" O   GLU J 207 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLU J 207 " --> pdb=" O   LEU J 368 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 226 through 228
      removed outlier: 3.504A  pdb=" N   VAL J 227 " --> pdb=" O   VAL J 343 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU J 342 " --> pdb=" O   GLU J 357 " (cutoff:3.500A)

    138 hydrogen bonds defined for protein.
    405 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: 2.27

  Time building geometry restraints manager: 5.99 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3931
        1.03 -     1.23: 7
        1.23 -     1.42: 1405
        1.42 -     1.61: 2365
        1.61 -     1.81: 39
  Bond restraints: 7747
  Sorted by residual:
  bond pdb=" C   ILE J 239 "
       pdb=" N   GLU J 240 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 1.40e-02 5.10e+03 2.71e-01
  bond pdb=" NE  ARG J 431 "
       pdb=" CZ  ARG J 431 "
    ideal  model  delta    sigma   weight residual
    1.326  1.331 -0.005 1.10e-02 8.26e+03 2.33e-01
  bond pdb=" C   VAL J 439 "
       pdb=" O   VAL J 439 "
    ideal  model  delta    sigma   weight residual
    1.236  1.242 -0.006 1.19e-02 7.06e+03 2.31e-01
  bond pdb=" C   ILE J 440 "
       pdb=" N   PRO J 441 "
    ideal  model  delta    sigma   weight residual
    1.337  1.343 -0.006 1.24e-02 6.50e+03 2.25e-01
  bond pdb=" CB  PRO J 441 "
       pdb=" CG  PRO J 441 "
    ideal  model  delta    sigma   weight residual
    1.492  1.471  0.021 5.00e-02 4.00e+02 1.82e-01
  ... (remaining 7742 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.98: 62
      106.98 -   113.05: 9881
      113.05 -   119.13: 1583
      119.13 -   125.20: 2568
      125.20 -   131.28: 51
  Bond angle restraints: 14145
  Sorted by residual:
  angle pdb=" CA  VAL J 439 "
        pdb=" C   VAL J 439 "
        pdb=" N   ILE J 440 "
      ideal   model   delta    sigma   weight residual
     116.60  119.38   -2.78 1.45e+00 4.76e-01 3.68e+00
  angle pdb=" N   VAL J 439 "
        pdb=" CA  VAL J 439 "
        pdb=" C   VAL J 439 "
      ideal   model   delta    sigma   weight residual
     109.34  113.02   -3.68 2.08e+00 2.31e-01 3.13e+00
  angle pdb=" CA  ALA J 201 "
        pdb=" C   ALA J 201 "
        pdb=" N   SER J 202 "
      ideal   model   delta    sigma   weight residual
     116.84  119.75   -2.91 1.71e+00 3.42e-01 2.89e+00
  angle pdb=" N   ALA J 201 "
        pdb=" CA  ALA J 201 "
        pdb=" C   ALA J 201 "
      ideal   model   delta    sigma   weight residual
     110.80  114.32   -3.52 2.13e+00 2.20e-01 2.73e+00
  angle pdb=" N   GLU J 240 "
        pdb=" CA  GLU J 240 "
        pdb=" C   GLU J 240 "
      ideal   model   delta    sigma   weight residual
     110.80  107.34    3.46 2.13e+00 2.20e-01 2.63e+00
  ... (remaining 14140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.94: 3333
       11.94 -    23.88: 124
       23.88 -    35.82: 35
       35.82 -    47.76: 22
       47.76 -    59.70: 22
  Dihedral angle restraints: 3536
    sinusoidal: 2036
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  LEU J 258 "
           pdb=" CB  LEU J 258 "
           pdb=" CG  LEU J 258 "
           pdb=" CD1 LEU J 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.07   40.93     3      1.50e+01 4.44e-03 7.31e+00
  dihedral pdb=" CA  LEU J 135 "
           pdb=" CB  LEU J 135 "
           pdb=" CG  LEU J 135 "
           pdb=" CD1 LEU J 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  144.83   35.17     3      1.50e+01 4.44e-03 6.01e+00
  dihedral pdb=" CA  LYS J 347 "
           pdb=" CB  LYS J 347 "
           pdb=" CG  LYS J 347 "
           pdb=" CD  LYS J 347 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   90.68  -30.68     3      1.50e+01 4.44e-03 4.91e+00
  ... (remaining 3533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 405
       0.024 -    0.048: 126
       0.048 -    0.072: 51
       0.072 -    0.096: 22
       0.096 -    0.120: 26
  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    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  VAL J 188 "
            pdb=" N   VAL J 188 "
            pdb=" C   VAL J 188 "
            pdb=" CB  VAL J 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  ILE J 195 "
            pdb=" N   ILE J 195 "
            pdb=" C   ILE J 195 "
            pdb=" CB  ILE J 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.47e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.006 5.00e-02 4.00e+02   9.72e-03 1.51e-01
        pdb=" N   PRO J 255 "    0.017 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J 255 "   -0.005 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET J 223 "    0.006 5.00e-02 4.00e+02   9.06e-03 1.31e-01
        pdb=" N   PRO J 224 "   -0.016 5.00e-02 4.00e+02
        pdb=" CA  PRO J 224 "    0.005 5.00e-02 4.00e+02
        pdb=" CD  PRO J 224 "    0.005 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY J  40 "    0.005 5.00e-02 4.00e+02   8.20e-03 1.08e-01
        pdb=" N   PRO J  41 "   -0.014 5.00e-02 4.00e+02
        pdb=" CA  PRO J  41 "    0.004 5.00e-02 4.00e+02
        pdb=" CD  PRO J  41 "    0.005 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 543
        2.24 -     2.83: 17924
        2.83 -     3.42: 17879
        3.42 -     4.01: 23299
        4.01 -     4.60: 36615
  Nonbonded interactions: 96260
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP J 451 "
            pdb=" H   GLU J 454 "
     model   vdw
     1.646 1.850
  nonbonded pdb=" OE1 GLU J 168 "
            pdb=" H   GLU J 168 "
     model   vdw
     1.652 1.850
  nonbonded pdb=" O   LEU J 317 "
            pdb=" HG1 THR J 321 "
     model   vdw
     1.713 1.850
  nonbonded pdb=" OE1 GLU J 245 "
            pdb=" H   GLU J 245 "
     model   vdw
     1.720 1.850
  nonbonded pdb=" OE1 GLU J  33 "
            pdb=" HE  ARG J  36 "
     model   vdw
     1.728 1.850
  ... (remaining 96255 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:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          4.720
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     27.280
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
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   0.021   3809  Z= 0.103
  Angle     :  0.353   5.628   5126  Z= 0.201
  Chirality :  0.037   0.120    630
  Planarity :  0.001   0.010    663
  Dihedral  :  4.651  40.926   1463
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 10.34 %
    Favored  : 89.07 %
  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: -4.05 (0.32), residues: 503
  helix: -3.25 (0.22), residues: 193
  sheet: -4.43 (0.45), residues: 62
  loop : -1.55 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 296 
 PHE   0.002   0.000   PHE J 261 
 TYR   0.001   0.000   TYR J 297 
 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
  51 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.4096
  time to fit residues: 25.4206
Evaluate side-chains
  29 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
J 132 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3809  Z= 0.156
  Angle     :  0.470   4.513   5126  Z= 0.259
  Chirality :  0.039   0.131    630
  Planarity :  0.002   0.013    663
  Dihedral  :  2.565  15.837    529
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.33), residues: 503
  helix: -1.32 (0.30), residues: 226
  sheet: -3.55 (0.51), residues: 68
  loop : -2.12 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J 375 
 PHE   0.005   0.001   PHE J 261 
 TYR   0.007   0.001   TYR J 124 
 ARG   0.003   0.000   ARG J 425 

*********************** 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
  33 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.3487
  time to fit residues: 14.6026
Evaluate side-chains
  23 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0870
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.9162

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3809  Z= 0.156
  Angle     :  0.421   4.332   5126  Z= 0.232
  Chirality :  0.037   0.118    630
  Planarity :  0.002   0.015    663
  Dihedral  :  2.604  12.595    529
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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: -1.87 (0.36), residues: 503
  helix: -0.23 (0.34), residues: 238
  sheet: -3.02 (0.64), residues: 58
  loop : -1.79 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J  72 
 PHE   0.006   0.001   PHE J 261 
 TYR   0.003   0.001   TYR J 418 
 ARG   0.003   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
  24 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2886
  time to fit residues: 9.6569
Evaluate side-chains
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
J 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3809  Z= 0.261
  Angle     :  0.492   4.138   5126  Z= 0.277
  Chirality :  0.037   0.116    630
  Planarity :  0.003   0.017    663
  Dihedral  :  3.083  14.986    529
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.38), residues: 503
  helix:  0.23 (0.34), residues: 238
  sheet: -2.73 (0.66), residues: 58
  loop : -1.51 (0.42), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 375 
 PHE   0.008   0.001   PHE J 261 
 TYR   0.003   0.001   TYR J 124 
 ARG   0.002   0.000   ARG J 346 

*********************** 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
  22 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2983
  time to fit residues: 9.2138
Evaluate side-chains
  18 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0570
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4795

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= 0.124
  Angle     :  0.372   4.013   5126  Z= 0.204
  Chirality :  0.037   0.122    630
  Planarity :  0.002   0.016    663
  Dihedral  :  2.766  12.584    529
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.38), residues: 503
  helix:  0.68 (0.35), residues: 239
  sheet: -2.53 (0.70), residues: 52
  loop : -1.21 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 463 
 PHE   0.007   0.001   PHE J 261 
 TYR   0.004   0.001   TYR J 297 
 ARG   0.001   0.000   ARG J 493 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2984
  time to fit residues: 9.0364
Evaluate side-chains
  19 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0050
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.3198

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3809  Z= 0.193
  Angle     :  0.422   4.146   5126  Z= 0.237
  Chirality :  0.037   0.123    630
  Planarity :  0.002   0.015    663
  Dihedral  :  3.042  13.559    529
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.39), residues: 503
  helix:  0.70 (0.34), residues: 241
  sheet: -2.29 (0.73), residues: 52
  loop : -1.15 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 375 
 PHE   0.006   0.001   PHE J 261 
 TYR   0.004   0.001   TYR J 297 
 ARG   0.002   0.000   ARG J 346 

*********************** 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
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.3233
  time to fit residues: 9.0483
Evaluate side-chains
  18 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
J  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3809  Z= 0.315
  Angle     :  0.539   4.567   5126  Z= 0.306
  Chirality :  0.038   0.145    630
  Planarity :  0.003   0.030    663
  Dihedral  :  3.702  14.993    529
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.36), residues: 503
  helix:  0.06 (0.32), residues: 243
  sheet: -2.42 (0.69), residues: 52
  loop : -1.22 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 116 
 PHE   0.010   0.002   PHE J 285 
 TYR   0.005   0.001   TYR J 297 
 ARG   0.005   0.001   ARG J 370 

*********************** 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
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.3069
  time to fit residues: 8.5986
Evaluate side-chains
  18 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.6037

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= 0.164
  Angle     :  0.411   4.571   5126  Z= 0.228
  Chirality :  0.037   0.120    630
  Planarity :  0.002   0.028    663
  Dihedral  :  3.353  13.958    529
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.37), residues: 503
  helix:  0.52 (0.33), residues: 241
  sheet: -2.30 (0.70), residues: 52
  loop : -1.16 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS J 463 
 PHE   0.005   0.001   PHE J 261 
 TYR   0.005   0.001   TYR J 297 
 ARG   0.004   0.000   ARG J 370 

*********************** 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
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.3064
  time to fit residues: 8.5811
Evaluate side-chains
  18 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0670
   chunk 45 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
J 132 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.6054

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= 0.119
  Angle     :  0.383   5.517   5126  Z= 0.207
  Chirality :  0.037   0.122    630
  Planarity :  0.002   0.028    663
  Dihedral  :  3.075  12.634    529
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.38), residues: 503
  helix:  1.06 (0.34), residues: 240
  sheet: -2.09 (0.73), residues: 52
  loop : -0.99 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.006   0.001   PHE J 261 
 TYR   0.004   0.001   TYR J 297 
 ARG   0.003   0.000   ARG J 370 

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

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  285 PHE cc_start: 0.8806 (m-80) cc_final: 0.8592 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.3105
  time to fit residues: 9.4802
Evaluate side-chains
  19 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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: 0.7824
moved from start:          0.6160

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= 0.142
  Angle     :  0.395   6.144   5126  Z= 0.216
  Chirality :  0.037   0.122    630
  Planarity :  0.002   0.030    663
  Dihedral  :  3.076  12.755    529
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.39), residues: 503
  helix:  1.13 (0.34), residues: 241
  sheet: -1.81 (0.71), residues: 58
  loop : -1.07 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.005   0.001   PHE J 261 
 TYR   0.003   0.001   TYR J 297 
 ARG   0.003   0.000   ARG J 370 

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

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

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

  1006 Ramachandran restraints generated.
    503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2930
  time to fit residues: 9.0669
Evaluate side-chains
  18 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.0870
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.054220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.036589 restraints weight = 78030.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.037944 restraints weight = 37529.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.038816 restraints weight = 22759.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.6177

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     :  0.375   6.199   5126  Z= 0.202
  Chirality :  0.037   0.125    630
  Planarity :  0.002   0.027    663
  Dihedral  :  2.938  12.301    529
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.39), residues: 503
  helix:  1.37 (0.35), residues: 240
  sheet: -1.44 (0.69), residues: 70
  loop : -0.96 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J 116 
 PHE   0.006   0.001   PHE J 261 
 TYR   0.002   0.000   TYR J 297 
 ARG   0.003   0.000   ARG J 370 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2376.32 seconds
wall clock time: 42 minutes 45.81 seconds (2565.81 seconds total)