Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 16:41:03 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/04_2022/7r9u_24331.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/04_2022/7r9u_24331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/04_2022/7r9u_24331.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/04_2022/7r9u_24331.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/04_2022/7r9u_24331.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/04_2022/7r9u_24331.pdb"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "J PHE  285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    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-4553/modules/chem_data/mon_lib"
  Total number of atoms: 7727
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "J"
      Number of atoms: 7727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 7727
          Classifications: {'peptide': 505}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 496}
  Time building chain proxies: 4.28, per 1000 atoms: 0.55
  Number of scatterers: 7727
  At special positions: 0
  Unit cell: (78.84, 72.36, 110.16, 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: 5.79
  Conformation dependent library (CDL) restraints added in 837.2 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
      51.7% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'J' and resid 21 through 37
      removed outlier: 4.005A  pdb=" N   ILE J  25 " --> pdb=" O   GLN J  21 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY J  28 " --> pdb=" O   ASN J  24 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG J  29 " --> pdb=" O   ILE J  25 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE J  31 " --> pdb=" O   ALA J  27 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   THR J  34 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL J  35 " --> pdb=" O   ILE J  31 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER J  37 " --> pdb=" O   GLU J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 60 through 68
      removed outlier: 3.932A  pdb=" N   ILE J  64 " --> pdb=" O   ASP J  60 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU J  65 " --> pdb=" O   GLY J  61 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU J  67 " --> pdb=" O   THR J  63 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 76 through 87
      removed outlier: 3.643A  pdb=" N   THR J  84 " --> pdb=" O   GLU J  80 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLN J  85 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLU J  86 " --> pdb=" O   ALA J  82 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS J  87 " --> pdb=" O   LYS J  83 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 93 through 113
      removed outlier: 3.634A  pdb=" N   VAL J  99 " --> pdb=" O   THR J  95 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY J 101 " --> pdb=" O   VAL J  97 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLU J 102 " --> pdb=" O   VAL J  98 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU J 103 " --> pdb=" O   VAL J  99 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU J 109 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLN J 113 " --> pdb=" O   GLU J 109 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 139
      removed outlier: 3.674A  pdb=" N   VAL J 120 " --> pdb=" O   HIS J 116 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY J 123 " --> pdb=" O   ILE J 119 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN J 132 " --> pdb=" O   ALA J 128 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLU J 133 " --> pdb=" O   GLN J 129 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU J 134 " --> pdb=" O   LYS J 130 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR J 137 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 146 through 159
      removed outlier: 3.608A  pdb=" N   LEU J 150 " --> pdb=" O   ASP J 146 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LYS J 152 " --> pdb=" O   GLU J 148 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE J 153 " --> pdb=" O   ILE J 149 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA J 154 " --> pdb=" O   LEU J 150 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   SER J 157 " --> pdb=" O   ILE J 153 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 169 through 181
      removed outlier: 3.562A  pdb=" N   GLU J 176 " --> pdb=" O   GLU J 172 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA J 177 " --> pdb=" O   ILE J 173 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA J 180 " --> pdb=" O   GLU J 176 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL J 181 " --> pdb=" O   ALA J 177 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 202 through 206
      removed outlier: 3.826A  pdb=" N   ASP J 205 " --> pdb=" O   SER J 202 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 260
      removed outlier: 3.711A  pdb=" N   MET J 259 " --> pdb=" O   ALA J 256 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU J 260 " --> pdb=" O   LYS J 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 256 through 260'
    Processing helix  chain 'J' and resid 262 through 279
      removed outlier: 3.787A  pdb=" N   GLU J 266 " --> pdb=" O   ILE J 262 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU J 269 " --> pdb=" O   GLU J 265 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS J 270 " --> pdb=" O   GLU J 266 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 293 through 301
      removed outlier: 4.145A  pdb=" N   TYR J 297 " --> pdb=" O   LEU J 293 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU J 298 " --> pdb=" O   ALA J 294 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA J 299 " --> pdb=" O   GLN J 295 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 322
      removed outlier: 4.255A  pdb=" N   LYS J 316 " --> pdb=" O   SER J 312 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR J 321 " --> pdb=" O   LEU J 317 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 373 through 398
      removed outlier: 3.576A  pdb=" N   ALA J 383 " --> pdb=" O   GLU J 379 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP J 385 " --> pdb=" O   ALA J 381 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP J 386 " --> pdb=" O   ARG J 382 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL J 388 " --> pdb=" O   VAL J 384 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY J 389 " --> pdb=" O   ASP J 385 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   THR J 394 " --> pdb=" O   VAL J 390 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 406 through 420
      removed outlier: 3.504A  pdb=" N   LEU J 411 " --> pdb=" O   THR J 407 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET J 413 " --> pdb=" O   VAL J 409 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS J 414 " --> pdb=" O   GLU J 410 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ARG J 416 " --> pdb=" O   SER J 412 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   GLU J 417 " --> pdb=" O   MET J 413 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU J 420 " --> pdb=" O   ARG J 416 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 423 through 425
      No H-bonds generated for 'chain 'J' and resid 423 through 425'
    Processing helix  chain 'J' and resid 426 through 435
    Processing helix  chain 'J' and resid 438 through 449
      removed outlier: 3.671A  pdb=" N   ARG J 442 " --> pdb=" O   GLU J 438 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU J 444 " --> pdb=" O   ILE J 440 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 454 through 463
      removed outlier: 3.955A  pdb=" N   LYS J 458 " --> pdb=" O   GLU J 454 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ARG J 460 " --> pdb=" O   LEU J 456 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA J 461 " --> pdb=" O   VAL J 457 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA J 462 " --> pdb=" O   LYS J 458 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   HIS J 463 " --> pdb=" O   VAL J 459 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 483 through 487
      removed outlier: 3.560A  pdb=" N   GLY J 487 " --> pdb=" O   MET J 483 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 483 through 487'
    Processing helix  chain 'J' and resid 492 through 511
      removed outlier: 3.628A  pdb=" N   THR J 496 " --> pdb=" O   LEU J 492 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA J 498 " --> pdb=" O   VAL J 494 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU J 507 " --> pdb=" O   ALA J 503 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   MET J 508 " --> pdb=" O   GLU J 504 " (cutoff:3.500A)
      removed outlier: 4.137A  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: 3.760A  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 199
      removed outlier: 6.619A  pdb=" N   LYS J 194 " --> pdb=" O   MET J 367 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ILE J 369 " --> pdb=" O   LYS J 194 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLU J 196 " --> pdb=" O   ILE J 369 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   GLY J 371 " --> pdb=" O   GLU J 196 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS J 198 " --> pdb=" O   GLY J 371 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR J 366 " --> pdb=" O   ILE J 209 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE J 209 " --> pdb=" O   THR J 366 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   LEU J 368 " --> pdb=" O   GLU J 207 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLU J 207 " --> pdb=" O   LEU J 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'J' and resid 212 through 214
      removed outlier: 3.776A  pdb=" N   ARG J 346 " --> pdb=" O   MET J 353 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 471 through 472
      removed outlier: 3.503A  pdb=" N   GLY J 472 " --> pdb=" O   GLU J 481 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU J 481 " --> pdb=" O   GLY J 472 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    121 hydrogen bonds defined for protein.
    351 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: 2.45

  Time building geometry restraints manager: 5.91 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=" N   GLY J 200 "
       pdb=" CA  GLY J 200 "
    ideal  model  delta    sigma   weight residual
    1.458  1.449  0.009 9.20e-03 1.18e+04 8.92e-01
  bond pdb=" CA  VAL J 219 "
       pdb=" C   VAL J 219 "
    ideal  model  delta    sigma   weight residual
    1.530  1.523  0.007 1.12e-02 7.97e+03 3.91e-01
  bond pdb=" CA  GLY J 200 "
       pdb=" C   GLY J 200 "
    ideal  model  delta    sigma   weight residual
    1.504  1.514 -0.011 1.83e-02 2.99e+03 3.48e-01
  bond pdb=" C   GLY J 200 "
       pdb=" O   GLY J 200 "
    ideal  model  delta    sigma   weight residual
    1.239  1.234  0.005 8.50e-03 1.38e+04 2.97e-01
  bond pdb=" N   LYS J  42 "
       pdb=" CA  LYS J  42 "
    ideal  model  delta    sigma   weight residual
    1.464  1.457  0.006 1.20e-02 6.94e+03 2.91e-01
  ... (remaining 7743 not shown)

  Histogram of bond angle deviations from ideal:
      100.79 -   106.89: 60
      106.89 -   112.98: 9862
      112.98 -   119.08: 1595
      119.08 -   125.18: 2576
      125.18 -   131.27: 54
  Bond angle restraints: 14147
  Sorted by residual:
  angle pdb=" N   VAL J 219 "
        pdb=" CA  VAL J 219 "
        pdb=" C   VAL J 219 "
      ideal   model   delta    sigma   weight residual
     111.91  109.75    2.16 8.90e-01 1.26e+00 5.89e+00
  angle pdb=" N   LYS J 330 "
        pdb=" CA  LYS J 330 "
        pdb=" C   LYS J 330 "
      ideal   model   delta    sigma   weight residual
     112.97  111.17    1.80 1.06e+00 8.90e-01 2.88e+00
  angle pdb=" C   ILE J 262 "
        pdb=" CA  ILE J 262 "
        pdb=" CB  ILE J 262 "
      ideal   model   delta    sigma   weight residual
     111.65  109.45    2.20 1.41e+00 5.03e-01 2.45e+00
  angle pdb=" C   VAL J  62 "
        pdb=" CA  VAL J  62 "
        pdb=" CB  VAL J  62 "
      ideal   model   delta    sigma   weight residual
     112.16  109.66    2.50 1.63e+00 3.76e-01 2.36e+00
  angle pdb=" CA  ILE J 440 "
        pdb=" C   ILE J 440 "
        pdb=" N   PRO J 441 "
      ideal   model   delta    sigma   weight residual
     118.88  120.92   -2.04 1.54e+00 4.22e-01 1.75e+00
  ... (remaining 14142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.82: 2844
        9.82 -    19.64: 125
       19.64 -    29.46: 22
       29.46 -    39.28: 9
       39.28 -    49.10: 2
  Dihedral angle restraints: 3002
    sinusoidal: 1501
      harmonic: 1501
  Sorted by residual:
  dihedral pdb=" CA  LEU J 284 "
           pdb=" CB  LEU J 284 "
           pdb=" CG  LEU J 284 "
           pdb=" CD1 LEU J 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  142.01   37.99     3      1.50e+01 4.44e-03 6.67e+00
  dihedral pdb=" CB  MET J 508 "
           pdb=" CG  MET J 508 "
           pdb=" SD  MET J 508 "
           pdb=" CE  MET J 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   95.72  -35.72     3      1.50e+01 4.44e-03 6.14e+00
  dihedral pdb=" CB  MET J 483 "
           pdb=" CG  MET J 483 "
           pdb=" SD  MET J 483 "
           pdb=" CE  MET J 483 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   92.54  -32.54     3      1.50e+01 4.44e-03 5.37e+00
  ... (remaining 2999 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 376
       0.024 -    0.048: 154
       0.048 -    0.072: 50
       0.072 -    0.097: 18
       0.097 -    0.121: 32
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ILE J 326 "
            pdb=" N   ILE J 326 "
            pdb=" C   ILE J 326 "
            pdb=" CB  ILE J 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  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 3.62e-01
  chirality pdb=" CA  VAL J 214 "
            pdb=" N   VAL J 214 "
            pdb=" C   VAL J 214 "
            pdb=" CB  VAL J 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 254 "   -0.011 5.00e-02 4.00e+02   1.68e-02 4.54e-01
        pdb=" N   PRO J 255 "    0.029 5.00e-02 4.00e+02
        pdb=" CA  PRO J 255 "   -0.009 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   HIS J 116 "    0.009 5.00e-02 4.00e+02   1.38e-02 3.03e-01
        pdb=" N   PRO J 117 "   -0.024 5.00e-02 4.00e+02
        pdb=" CA  PRO J 117 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO J 117 "    0.008 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   9.61e-03 1.48e-01
        pdb=" N   PRO J 224 "   -0.017 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
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 526
        2.23 -     2.83: 17885
        2.83 -     3.42: 17716
        3.42 -     4.01: 22870
        4.01 -     4.60: 36498
  Nonbonded interactions: 95495
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU J 168 "
            pdb=" H   GLU J 168 "
     model   vdw
     1.642 1.850
  nonbonded pdb="HD21 ASN J 328 "
            pdb=" OD2 ASP J 331 "
     model   vdw
     1.696 1.850
  nonbonded pdb=" OD1 ASP J 183 "
            pdb=" H   LYS J 187 "
     model   vdw
     1.744 1.850
  nonbonded pdb=" OE1 GLU J 172 "
            pdb=" H   GLU J 172 "
     model   vdw
     1.749 1.850
  nonbonded pdb=" O   LYS J 152 "
            pdb=" HG1 THR J 156 "
     model   vdw
     1.757 1.850
  ... (remaining 95490 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
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.
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:             0.820
  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:          5.000
  Check model and map are aligned:         0.120
  Convert atoms to be neutral:             0.070
  Process input model:                     27.540
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Set scattering table:                    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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6227
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= 0.100
  Angle     :  0.342   3.797   5126  Z= 0.205
  Chirality :  0.038   0.121    630
  Planarity :  0.001   0.017    663
  Dihedral  :  4.356  37.994   1463
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  9.15 %
    Favored  : 90.26 %
  Rotamer Outliers :  0.00 %
  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: -4.49 (0.31), residues: 503
  helix: -3.85 (0.20), residues: 184
  sheet: -3.70 (0.54), residues: 57
  loop : -2.04 (0.36), residues: 262

*********************** 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
  56 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.736 
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: 56
  average time/residue: 0.3436
  time to fit residues: 24.0576
Evaluate side-chains
  32 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.662 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8233
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
J 447 ASN
J 474 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3809  Z= 0.190
  Angle     :  0.499   4.811   5126  Z= 0.276
  Chirality :  0.039   0.130    630
  Planarity :  0.003   0.025    663
  Dihedral  :  2.727  11.663    529
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.78 %
    Favored  : 96.02 %
  Rotamer Outliers :  0.00 %
  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: -2.79 (0.34), residues: 503
  helix: -1.66 (0.31), residues: 216
  sheet: -3.16 (0.54), residues: 59
  loop : -1.48 (0.40), residues: 228

*********************** 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
  34 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.691 
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: 34
  average time/residue: 0.3782
  time to fit residues: 16.3362
Evaluate side-chains
  26 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.647 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7871
-------------------------------------------------------------------------------
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:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
J  24 ASN
J 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3809  Z= 0.205
  Angle     :  0.494   4.355   5126  Z= 0.276
  Chirality :  0.038   0.125    630
  Planarity :  0.003   0.029    663
  Dihedral  :  3.041  12.423    529
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer Outliers :  0.00 %
  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: -1.44 (0.35), residues: 503
  helix: -0.34 (0.32), residues: 217
  sheet: -1.86 (0.63), residues: 55
  loop : -1.22 (0.41), residues: 231

*********************** 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: 0
    poor density    : 28
  time to evaluate  : 0.622 
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: 28
  average time/residue: 0.4638
  time to fit residues: 15.9263
Evaluate side-chains
  24 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.680 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7515
-------------------------------------------------------------------------------
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:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    0.3980
   chunk 21 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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: 0.6682
moved from start:          0.4586

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     :  0.379   4.193   5126  Z= 0.207
  Chirality :  0.038   0.131    630
  Planarity :  0.002   0.022    663
  Dihedral  :  2.788  11.918    529
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer Outliers :  0.00 %
  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: -0.60 (0.37), residues: 503
  helix:  0.47 (0.34), residues: 217
  sheet: -1.45 (0.74), residues: 45
  loop : -0.94 (0.41), residues: 241

*********************** 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
  23 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.732 
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: 23
  average time/residue: 0.4223
  time to fit residues: 12.4687
Evaluate side-chains
  23 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.682 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8491
-------------------------------------------------------------------------------
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:    5.9990
   chunk 19 optimal weight:    0.0270
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.1042

-------------------------------------------------------------------------------
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: 0.6774
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3809  Z= 0.163
  Angle     :  0.422   4.201   5126  Z= 0.235
  Chirality :  0.037   0.129    630
  Planarity :  0.002   0.030    663
  Dihedral  :  2.902  12.514    529
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer Outliers :  0.00 %
  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: -0.26 (0.38), residues: 503
  helix:  0.84 (0.35), residues: 218
  sheet: -1.14 (0.71), residues: 55
  loop : -0.85 (0.43), residues: 230

*********************** 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
  23 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.678 
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: 23
  average time/residue: 0.3798
  time to fit residues: 11.3214
Evaluate side-chains
  21 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.736 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7219
-------------------------------------------------------------------------------
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:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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: 0.6810
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3809  Z= 0.158
  Angle     :  0.420   4.164   5126  Z= 0.233
  Chirality :  0.037   0.136    630
  Planarity :  0.002   0.031    663
  Dihedral  :  2.942  12.122    529
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer Outliers :  0.00 %
  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 (0.38), residues: 503
  helix:  0.99 (0.35), residues: 224
  sheet: -1.02 (0.73), residues: 55
  loop : -0.83 (0.43), residues: 224

*********************** 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
  23 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.671 
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: 23
  average time/residue: 0.3627
  time to fit residues: 11.1151
Evaluate side-chains
  21 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.697 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8616
-------------------------------------------------------------------------------
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:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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: 0.6890
moved from start:          0.6117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3809  Z= 0.201
  Angle     :  0.457   4.053   5126  Z= 0.256
  Chirality :  0.037   0.129    630
  Planarity :  0.003   0.037    663
  Dihedral  :  3.255  13.637    529
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer Outliers :  0.00 %
  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: -0.17 (0.37), residues: 503
  helix:  0.93 (0.34), residues: 224
  sheet: -0.94 (0.72), residues: 55
  loop : -0.90 (0.42), residues: 224

*********************** 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  : 0.679 
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: 0.3516
  time to fit residues: 9.5566
Evaluate side-chains
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.700 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8642
-------------------------------------------------------------------------------
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:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    0.2980
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0570
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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: 0.6812
moved from start:          0.6085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3809  Z= 0.103
  Angle     :  0.375   4.103   5126  Z= 0.204
  Chirality :  0.038   0.128    630
  Planarity :  0.002   0.029    663
  Dihedral  :  2.975  12.301    529
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer Outliers :  0.00 %
  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:  0.21 (0.38), residues: 503
  helix:  1.23 (0.34), residues: 225
  sheet: -0.70 (0.82), residues: 45
  loop : -0.72 (0.41), residues: 233

*********************** 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
  22 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.705 
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: 22
  average time/residue: 0.3455
  time to fit residues: 10.2443
Evaluate side-chains
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.631 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8130
-------------------------------------------------------------------------------
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:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0060
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
J  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.6323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3809  Z= 0.139
  Angle     :  0.399   4.038   5126  Z= 0.222
  Chirality :  0.037   0.127    630
  Planarity :  0.002   0.033    663
  Dihedral  :  3.036  12.680    529
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer Outliers :  0.00 %
  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:  0.20 (0.37), residues: 503
  helix:  1.21 (0.34), residues: 226
  sheet: -0.73 (0.82), residues: 45
  loop : -0.72 (0.40), residues: 232

*********************** 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
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.705 
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: 0.3531
  time to fit residues: 9.5622
Evaluate side-chains
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.682 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8562
-------------------------------------------------------------------------------
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:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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: 0.6836
moved from start:          0.6368

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= 0.106
  Angle     :  0.375   4.153   5126  Z= 0.205
  Chirality :  0.038   0.124    630
  Planarity :  0.002   0.031    663
  Dihedral  :  2.953  12.472    529
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer Outliers :  0.00 %
  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:  0.32 (0.38), residues: 503
  helix:  1.30 (0.34), residues: 226
  sheet: -0.70 (0.83), residues: 45
  loop : -0.64 (0.41), residues: 232

********************** 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
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.712 
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: 0.3368
  time to fit residues: 9.1401
Evaluate side-chains
  20 residues out of total 407 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.685 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7599
-------------------------------------------------------------------------------
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:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   chunk 45 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3237 r_free = 0.3237 target = 0.042293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.029233 restraints weight = 107430.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.030350 restraints weight = 56712.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.031124 restraints weight = 36163.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.6577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3809  Z= 0.138
  Angle     :  0.398   4.180   5126  Z= 0.221
  Chirality :  0.037   0.123    630
  Planarity :  0.002   0.033    663
  Dihedral  :  3.039  12.428    529
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer Outliers :  0.00 %
  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:  0.26 (0.37), residues: 503
  helix:  1.22 (0.34), residues: 228
  sheet: -0.75 (0.81), residues: 45
  loop : -0.66 (0.40), residues: 230

===============================================================================
Job complete
usr+sys time: 2462.68 seconds
wall clock time: 43 minutes 54.69 seconds (2634.69 seconds total)