Starting phenix.real_space_refine
on Wed Sep 17 14:26:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iol_60744/09_2025/9iol_60744.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iol_60744/09_2025/9iol_60744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iol_60744/09_2025/9iol_60744.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iol_60744/09_2025/9iol_60744.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iol_60744/09_2025/9iol_60744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iol_60744/09_2025/9iol_60744.map"
  }
  resolution = 3.46
  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
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=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic.
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
     P      46      5.49       5
     S      40      5.16       5
     C    5631      2.51       5
     N    1530      2.21       5
     O    1789      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4104
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 23, 'TRANS': 488}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3970
          Classifications: {'peptide': 494}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 27, 'TRANS': 466}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 404
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 416
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "M"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 101
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'2OP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'2OP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.38, per 1000 atoms: 0.26
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (95.57, 92.7029, 141.444, 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      40     16.00
     P      46     15.00
     O    1789      8.00
     N    1530      7.00
     C    5631      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 338.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      39.7% alpha, 20.9% beta
      12 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 48
    Processing helix  chain 'A' and resid 87 through 96
    Processing helix  chain 'A' and resid 106 through 123
      removed outlier: 3.676A  pdb=" N   ILE A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 157
    Processing helix  chain 'A' and resid 198 through 222
      removed outlier: 9.357A  pdb=" N   GLU A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASP A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'A' and resid 299 through 303
      removed outlier: 4.543A  pdb=" N   THR A 303 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 308
      No H-bonds generated for 'chain 'A' and resid 306 through 308'
    Processing helix  chain 'A' and resid 324 through 332
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 352 through 356
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 3.829A  pdb=" N   LEU A 430 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 461
      removed outlier: 3.582A  pdb=" N   ASP A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 482
      removed outlier: 3.574A  pdb=" N   ILE A 482 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 500
      removed outlier: 3.702A  pdb=" N   GLN A 488 " --> pdb=" O   ASN A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 517
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'A' and resid 526 through 537
    Processing helix  chain 'B' and resid 45 through 50
    Processing helix  chain 'B' and resid 58 through 78
    Processing helix  chain 'B' and resid 112 through 121
    Processing helix  chain 'B' and resid 123 through 136
    Processing helix  chain 'B' and resid 142 through 156
    Processing helix  chain 'B' and resid 179 through 196
    Processing helix  chain 'B' and resid 238 through 251
      removed outlier: 3.935A  pdb=" N   THR B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 314
      No H-bonds generated for 'chain 'B' and resid 312 through 314'
    Processing helix  chain 'B' and resid 330 through 338
      removed outlier: 3.788A  pdb=" N   LYS B 338 " --> pdb=" O   THR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 356
      No H-bonds generated for 'chain 'B' and resid 354 through 356'
    Processing helix  chain 'B' and resid 377 through 393
      removed outlier: 3.538A  pdb=" N   LEU B 381 " --> pdb=" O   GLY B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 443
    Processing helix  chain 'B' and resid 455 through 469
    Processing helix  chain 'B' and resid 474 through 478
      removed outlier: 4.159A  pdb=" N   PHE B 478 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 495
      removed outlier: 3.537A  pdb=" N   ARG B 488 " --> pdb=" O   GLN B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 519
    Processing helix  chain 'B' and resid 520 through 530
    Processing helix  chain 'M' and resid 9 through 13
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84
      removed outlier: 5.194A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU A  58 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LEU A  83 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE A  54 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ALA A  55 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL A  10 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   VAL A  57 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   LEU A  12 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   PHE A  59 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   MET A  14 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ARG A 130 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   GLN A 162 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE A 132 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   PHE A 164 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE A 134 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR A 225 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 165 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253
      removed outlier: 6.913A  pdb=" N   VAL A 361 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LEU A 268 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   ASN A 359 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   ASN A 359 " --> pdb=" O   TYR A 421 " (cutoff:3.500A)
      removed outlier: 11.930A  pdb=" N   TYR A 421 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 10.122A  pdb=" N   VAL A 361 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 11.031A  pdb=" N   LEU A 419 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 9.948A  pdb=" N   LYS A 363 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
      removed outlier: 10.850A  pdb=" N   GLU A 417 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   MET A 389 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLY A 344 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ARG A 394 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   VAL A 342 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   ALA A 396 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   PHE A 340 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 280
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 297
    Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322
    Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA7, first strand: chain 'A' and resid 540 through 541
    Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109
      removed outlier: 7.161A  pdb=" N   LEU B 105 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 8.779A  pdb=" N   PHE B  87 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   GLU B 107 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   VAL B  85 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP B  43 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS B 164 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 8.724A  pdb=" N   ASP B 201 " --> pdb=" O   LYS B 164 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE B 166 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   MET B 203 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 168 " --> pdb=" O   MET B 203 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262
      removed outlier: 7.825A  pdb=" N   VAL B 394 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 350 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   PHE B 350 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B 397 " --> pdb=" O   MET B 348 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 420
      removed outlier: 6.882A  pdb=" N   GLU B 419 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1428
        1.29 -     1.42: 2464
        1.42 -     1.55: 5244
        1.55 -     1.69: 89
        1.69 -     1.82: 67
  Bond restraints: 9292
  Sorted by residual:
  bond pdb=" CB  GLN B 320 "
       pdb=" CG  GLN B 320 "
    ideal  model  delta    sigma   weight residual
    1.520  1.340  0.180 3.00e-02 1.11e+03 3.59e+01
  bond pdb=" CZ  ARG B 318 "
       pdb=" NH2 ARG B 318 "
    ideal  model  delta    sigma   weight residual
    1.330  1.259  0.071 1.30e-02 5.92e+03 3.00e+01
  bond pdb=" O14 IHP B 801 "
       pdb=" P4  IHP B 801 "
    ideal  model  delta    sigma   weight residual
    1.671  1.571  0.100 2.00e-02 2.50e+03 2.49e+01
  bond pdb=" CZ  ARG B 318 "
       pdb=" NH1 ARG B 318 "
    ideal  model  delta    sigma   weight residual
    1.323  1.260  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" O12 IHP B 801 "
       pdb=" P2  IHP B 801 "
    ideal  model  delta    sigma   weight residual
    1.675  1.586  0.089 2.00e-02 2.50e+03 1.96e+01
  ... (remaining 9287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.09: 12400
        4.09 -     8.18: 302
        8.18 -    12.27: 5
       12.27 -    16.36: 1
       16.36 -    20.45: 1
  Bond angle restraints: 12709
  Sorted by residual:
  angle pdb=" CB  GLN B 320 "
        pdb=" CG  GLN B 320 "
        pdb=" CD  GLN B 320 "
      ideal   model   delta    sigma   weight residual
     112.60  133.05  -20.45 1.70e+00 3.46e-01 1.45e+02
  angle pdb=" CA  GLN B 320 "
        pdb=" CB  GLN B 320 "
        pdb=" CG  GLN B 320 "
      ideal   model   delta    sigma   weight residual
     114.10  126.57  -12.47 2.00e+00 2.50e-01 3.89e+01
  angle pdb=" OE1 GLN B 320 "
        pdb=" CD  GLN B 320 "
        pdb=" NE2 GLN B 320 "
      ideal   model   delta    sigma   weight residual
     122.60  117.36    5.24 1.00e+00 1.00e+00 2.74e+01
  angle pdb=" O   GLY A 313 "
        pdb=" C   GLY A 313 "
        pdb=" N   PHE A 314 "
      ideal   model   delta    sigma   weight residual
     123.65  118.92    4.73 9.20e-01 1.18e+00 2.64e+01
  angle pdb=" C4'  DA D   7 "
        pdb=" C3'  DA D   7 "
        pdb=" O3'  DA D   7 "
      ideal   model   delta    sigma   weight residual
     110.00  102.35    7.65 1.50e+00 4.44e-01 2.60e+01
  ... (remaining 12704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.39: 5110
       23.39 -    46.77: 372
       46.77 -    70.15: 121
       70.15 -    93.54: 14
       93.54 -   116.92: 4
  Dihedral angle restraints: 5621
    sinusoidal: 2627
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" C   LEU A 108 "
           pdb=" N   LEU A 108 "
           pdb=" CA  LEU A 108 "
           pdb=" CB  LEU A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.02   14.42     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" CA  LYS A 413 "
           pdb=" C   LYS A 413 "
           pdb=" N   HIS A 414 "
           pdb=" CA  HIS A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.25   28.75     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  GLU B  91 "
           pdb=" C   GLU B  91 "
           pdb=" N   LYS B  92 "
           pdb=" CA  LYS B  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.09   25.91     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5618 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1179
       0.107 -    0.215: 217
       0.215 -    0.322: 30
       0.322 -    0.429: 2
       0.429 -    0.536: 2
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CA  LEU A 108 "
            pdb=" N   LEU A 108 "
            pdb=" C   LEU A 108 "
            pdb=" CB  LEU A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.20e+00
  chirality pdb=" CA  PHE B 159 "
            pdb=" N   PHE B 159 "
            pdb=" C   PHE B 159 "
            pdb=" CB  PHE B 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CG  LEU B  57 "
            pdb=" CB  LEU B  57 "
            pdb=" CD1 LEU B  57 "
            pdb=" CD2 LEU B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.20   -0.39 2.00e-01 2.50e+01 3.76e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA D   1 "    0.355 2.00e-02 2.50e+03   1.51e-01 6.30e+02
        pdb=" N9   DA D   1 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8   DA D   1 "   -0.095 2.00e-02 2.50e+03
        pdb=" N7   DA D   1 "   -0.097 2.00e-02 2.50e+03
        pdb=" C5   DA D   1 "   -0.093 2.00e-02 2.50e+03
        pdb=" C6   DA D   1 "    0.028 2.00e-02 2.50e+03
        pdb=" N6   DA D   1 "    0.242 2.00e-02 2.50e+03
        pdb=" N1   DA D   1 "    0.030 2.00e-02 2.50e+03
        pdb=" C2   DA D   1 "   -0.053 2.00e-02 2.50e+03
        pdb=" N3   DA D   1 "   -0.114 2.00e-02 2.50e+03
        pdb=" C4   DA D   1 "   -0.133 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  14 "   -0.188 2.00e-02 2.50e+03   1.22e-01 3.72e+02
        pdb=" N1   DT C  14 "    0.121 2.00e-02 2.50e+03
        pdb=" C2   DT C  14 "    0.141 2.00e-02 2.50e+03
        pdb=" O2   DT C  14 "   -0.141 2.00e-02 2.50e+03
        pdb=" N3   DT C  14 "    0.128 2.00e-02 2.50e+03
        pdb=" C4   DT C  14 "    0.022 2.00e-02 2.50e+03
        pdb=" O4   DT C  14 "   -0.155 2.00e-02 2.50e+03
        pdb=" C5   DT C  14 "    0.035 2.00e-02 2.50e+03
        pdb=" C7   DT C  14 "   -0.073 2.00e-02 2.50e+03
        pdb=" C6   DT C  14 "    0.108 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC C   7 "   -0.155 2.00e-02 2.50e+03   8.46e-02 1.61e+02
        pdb=" N1   DC C   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DC C   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DC C   7 "    0.119 2.00e-02 2.50e+03
        pdb=" N3   DC C   7 "   -0.036 2.00e-02 2.50e+03
        pdb=" C4   DC C   7 "   -0.028 2.00e-02 2.50e+03
        pdb=" N4   DC C   7 "   -0.081 2.00e-02 2.50e+03
        pdb=" C5   DC C   7 "    0.077 2.00e-02 2.50e+03
        pdb=" C6   DC C   7 "    0.109 2.00e-02 2.50e+03
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1288
        2.79 -     3.31: 9097
        3.31 -     3.84: 14986
        3.84 -     4.37: 17397
        4.37 -     4.90: 28012
  Nonbonded interactions: 70780
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 324 "
            pdb=" OD2 ASP A 327 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG1 THR A  61 "
            pdb=" O   GLY A  63 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LYS B 265 "
            pdb=" NZ  LYS B 265 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   GLY A  17 "
            pdb=" OG  SER A  21 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ILE A 197 "
            pdb=" NZ  LYS A 202 "
     model   vdw
     2.345 3.120
  ... (remaining 70775 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.910
  Find NCS groups from input model:        0.050
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
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      :  0.012   0.180   9293  Z= 0.657
  Angle     :  1.665  20.454  12709  Z= 1.075
  Chirality :  0.085   0.536   1430
  Planarity :  0.017   0.173   1482
  Dihedral  : 18.011 116.920   3667
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.85 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.24), residues: 1007
  helix: -0.29 (0.25), residues: 354
  sheet:  0.52 (0.38), residues: 156
  loop : -0.57 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 165 
 TYR   0.111   0.015   TYR B 217 
 PHE   0.060   0.010   PHE A 409 
 TRP   0.077   0.016   TRP A 276 
 HIS   0.014   0.003   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.01171 ( 9292)
  covalent geometry    : angle       1.66530 (12709)
  hydrogen bonds       : bond        0.15671 (  403)
  hydrogen bonds       : angle       7.91297 ( 1092)
  Misc. bond           : bond        0.01948 (    1)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9320 (mmt) cc_final: 0.8968 (mmm)
REVERT: A  208 VAL cc_start: 0.9637 (t) cc_final: 0.9428 (t)
REVERT: A  292 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7806 (tm-30)
REVERT: A  427 MET cc_start: 0.9567 (tmm) cc_final: 0.9040 (tmm)
REVERT: A  461 MET cc_start: 0.9015 (mpp) cc_final: 0.8790 (mmp)
REVERT: B   41 LEU cc_start: 0.9299 (mm) cc_final: 0.9076 (mm)
REVERT: B   62 MET cc_start: 0.9120 (tpp) cc_final: 0.8805 (tpp)
REVERT: B   68 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9225 (mm-40)
REVERT: B  287 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8898 (mmmt)
REVERT: B  488 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8961 (tpp80)
REVERT: B  514 MET cc_start: 0.9705 (mtp) cc_final: 0.9173 (mtp)
REVERT: B  518 LEU cc_start: 0.9683 (mt) cc_final: 0.9448 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 90
  average time/residue: 0.1066
  time to fit residues: 13.3627
Evaluate side-chains
  69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  488 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 432 GLN
B  68 GLN
B 152 ASN
B 176 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.059376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.041073 restraints weight = 43193.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 4.87
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9293  Z= 0.168
  Angle     :  0.673   6.615  12709  Z= 0.356
  Chirality :  0.044   0.178   1430
  Planarity :  0.004   0.044   1482
  Dihedral  : 19.382 103.876   1568
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.03 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.25), residues: 1007
  helix:  0.82 (0.27), residues: 354
  sheet:  0.32 (0.37), residues: 165
  loop : -0.41 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M   9 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.018   0.002   PHE A  31 
 TRP   0.016   0.002   TRP A 247 
 HIS   0.005   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9292)
  covalent geometry    : angle       0.67317 (12709)
  hydrogen bonds       : bond        0.05688 (  403)
  hydrogen bonds       : angle       5.85053 ( 1092)
  Misc. bond           : bond        0.00024 (    1)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9353 (mmt) cc_final: 0.9039 (mmm)
REVERT: A  427 MET cc_start: 0.9618 (tmm) cc_final: 0.9090 (tmm)
REVERT: A  461 MET cc_start: 0.9119 (mpp) cc_final: 0.8814 (mmp)
REVERT: B   62 MET cc_start: 0.9145 (tpp) cc_final: 0.8908 (tpp)
REVERT: B  287 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8883 (mmmt)
REVERT: B  518 LEU cc_start: 0.9692 (mt) cc_final: 0.9463 (mt)
  outliers start: 13
  outliers final: 4
  residues processed: 76
  average time/residue: 0.0915
  time to fit residues: 10.1234
Evaluate side-chains
  68 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 22 optimal weight:    0.1980
   chunk 18 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 517 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.058826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.040430 restraints weight = 43592.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 4.94
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9293  Z= 0.168
  Angle     :  0.622   6.945  12709  Z= 0.326
  Chirality :  0.042   0.152   1430
  Planarity :  0.004   0.047   1482
  Dihedral  : 18.983 101.364   1554
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.45 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.25), residues: 1007
  helix:  1.14 (0.27), residues: 355
  sheet:  0.28 (0.38), residues: 167
  loop : -0.35 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.011   0.001   TYR B 217 
 PHE   0.028   0.002   PHE A  31 
 TRP   0.010   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9292)
  covalent geometry    : angle       0.62222 (12709)
  hydrogen bonds       : bond        0.04966 (  403)
  hydrogen bonds       : angle       5.38981 ( 1092)
  Misc. bond           : bond        0.00023 (    1)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9412 (tpp) cc_final: 0.9203 (tpp)
REVERT: A  427 MET cc_start: 0.9655 (tmm) cc_final: 0.9113 (tmm)
REVERT: A  461 MET cc_start: 0.9191 (mpp) cc_final: 0.8779 (mmp)
REVERT: B   62 MET cc_start: 0.9177 (tpp) cc_final: 0.8849 (tpp)
REVERT: B  518 LEU cc_start: 0.9665 (mt) cc_final: 0.9427 (mt)
  outliers start: 7
  outliers final: 4
  residues processed: 71
  average time/residue: 0.0921
  time to fit residues: 9.6490
Evaluate side-chains
  71 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  307 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 1 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 415 ASN
A 452 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.057820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.039313 restraints weight = 45211.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.2767 rms_B_bonded: 4.93
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9293  Z= 0.227
  Angle     :  0.642   7.297  12709  Z= 0.337
  Chirality :  0.043   0.180   1430
  Planarity :  0.004   0.051   1482
  Dihedral  : 18.856  96.963   1554
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.00 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.26), residues: 1007
  helix:  1.25 (0.28), residues: 355
  sheet:  0.21 (0.39), residues: 160
  loop : -0.37 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG M   9 
 TYR   0.010   0.001   TYR B 217 
 PHE   0.018   0.002   PHE A  31 
 TRP   0.007   0.001   TRP A 247 
 HIS   0.004   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 9292)
  covalent geometry    : angle       0.64187 (12709)
  hydrogen bonds       : bond        0.05106 (  403)
  hydrogen bonds       : angle       5.28144 ( 1092)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8758 (t) cc_final: 0.8442 (t)
REVERT: A  163 PHE cc_start: 0.8572 (m-80) cc_final: 0.8372 (m-80)
REVERT: A  427 MET cc_start: 0.9661 (tmm) cc_final: 0.9170 (tmm)
REVERT: A  461 MET cc_start: 0.9159 (tpp) cc_final: 0.8929 (mmp)
REVERT: B   62 MET cc_start: 0.9160 (tpp) cc_final: 0.8751 (tpp)
REVERT: B  203 MET cc_start: 0.9476 (mmp) cc_final: 0.9152 (mmp)
REVERT: B  518 LEU cc_start: 0.9651 (mt) cc_final: 0.9419 (mt)
REVERT: M    9 ARG cc_start: 0.8898 (ptm-80) cc_final: 0.8634 (ptm-80)
  outliers start: 17
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0876
  time to fit residues: 10.4208
Evaluate side-chains
  76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0470
   chunk 79 optimal weight:    0.7980
   chunk 72 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   overall best weight:    3.3684

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.057483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.039070 restraints weight = 45272.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 4.91
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9293  Z= 0.208
  Angle     :  0.640   8.007  12709  Z= 0.331
  Chirality :  0.043   0.215   1430
  Planarity :  0.004   0.050   1482
  Dihedral  : 18.689  92.843   1554
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.20 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.26), residues: 1007
  helix:  1.31 (0.27), residues: 355
  sheet:  0.25 (0.39), residues: 160
  loop : -0.42 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M   9 
 TYR   0.012   0.001   TYR B 217 
 PHE   0.017   0.002   PHE A  31 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.004   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9292)
  covalent geometry    : angle       0.64011 (12709)
  hydrogen bonds       : bond        0.04828 (  403)
  hydrogen bonds       : angle       5.13091 ( 1092)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8675 (t) cc_final: 0.8070 (t)
REVERT: A  427 MET cc_start: 0.9667 (tmm) cc_final: 0.9166 (tmm)
REVERT: B   62 MET cc_start: 0.9134 (tpp) cc_final: 0.8814 (tpp)
REVERT: B  203 MET cc_start: 0.9534 (mmp) cc_final: 0.9264 (mmp)
REVERT: B  497 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9087 (pp)
REVERT: B  518 LEU cc_start: 0.9619 (mt) cc_final: 0.9388 (mt)
  outliers start: 18
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0870
  time to fit residues: 10.1598
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 66 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.058578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.040233 restraints weight = 43733.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 4.92
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9293  Z= 0.126
  Angle     :  0.627  11.926  12709  Z= 0.312
  Chirality :  0.041   0.241   1430
  Planarity :  0.003   0.048   1482
  Dihedral  : 18.545  89.096   1554
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.41 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.26), residues: 1007
  helix:  1.44 (0.28), residues: 356
  sheet:  0.29 (0.40), residues: 160
  loop : -0.32 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M   9 
 TYR   0.010   0.001   TYR B 217 
 PHE   0.017   0.001   PHE A  31 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9292)
  covalent geometry    : angle       0.62697 (12709)
  hydrogen bonds       : bond        0.04389 (  403)
  hydrogen bonds       : angle       4.94764 ( 1092)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9518 (tpp) cc_final: 0.9224 (tpp)
REVERT: A  134 ILE cc_start: 0.9110 (mm) cc_final: 0.8808 (tt)
REVERT: A  427 MET cc_start: 0.9650 (tmm) cc_final: 0.9219 (tmm)
REVERT: A  461 MET cc_start: 0.9187 (tpp) cc_final: 0.8790 (mmp)
REVERT: B   62 MET cc_start: 0.9085 (tpp) cc_final: 0.8745 (tpp)
REVERT: B  203 MET cc_start: 0.9388 (mmp) cc_final: 0.9048 (mmp)
REVERT: B  497 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9084 (pp)
REVERT: B  518 LEU cc_start: 0.9616 (mt) cc_final: 0.9391 (mt)
  outliers start: 14
  outliers final: 10
  residues processed: 75
  average time/residue: 0.0834
  time to fit residues: 9.5175
Evaluate side-chains
  75 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.058146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.039840 restraints weight = 44815.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 4.90
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9293  Z= 0.160
  Angle     :  0.631  10.895  12709  Z= 0.314
  Chirality :  0.041   0.242   1430
  Planarity :  0.003   0.049   1482
  Dihedral  : 18.399  85.412   1554
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.87 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.26), residues: 1007
  helix:  1.50 (0.28), residues: 355
  sheet:  0.26 (0.40), residues: 160
  loop : -0.35 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M   9 
 TYR   0.010   0.001   TYR B 217 
 PHE   0.024   0.001   PHE A  31 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9292)
  covalent geometry    : angle       0.63123 (12709)
  hydrogen bonds       : bond        0.04376 (  403)
  hydrogen bonds       : angle       4.89114 ( 1092)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9485 (tpp) cc_final: 0.9201 (tpp)
REVERT: A  134 ILE cc_start: 0.9076 (mm) cc_final: 0.8811 (tt)
REVERT: A  427 MET cc_start: 0.9663 (tmm) cc_final: 0.9224 (tmm)
REVERT: A  461 MET cc_start: 0.9189 (tpp) cc_final: 0.8725 (mpp)
REVERT: B  203 MET cc_start: 0.9560 (mmp) cc_final: 0.9037 (mmp)
REVERT: B  469 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: B  497 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9117 (pp)
  outliers start: 20
  outliers final: 13
  residues processed: 77
  average time/residue: 0.0829
  time to fit residues: 9.7180
Evaluate side-chains
  76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
A 511 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.059278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.040998 restraints weight = 43975.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.90
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9293  Z= 0.116
  Angle     :  0.658  12.104  12709  Z= 0.320
  Chirality :  0.042   0.248   1430
  Planarity :  0.003   0.047   1482
  Dihedral  : 18.275  81.341   1554
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.18 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1007
  helix:  1.50 (0.28), residues: 355
  sheet:  0.34 (0.40), residues: 160
  loop : -0.28 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M   9 
 TYR   0.010   0.001   TYR B 217 
 PHE   0.018   0.001   PHE A 227 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.002   0.000   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9292)
  covalent geometry    : angle       0.65781 (12709)
  hydrogen bonds       : bond        0.04067 (  403)
  hydrogen bonds       : angle       4.84396 ( 1092)
  Misc. bond           : bond        0.00002 (    1)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9475 (tpp) cc_final: 0.9190 (tpp)
REVERT: A  427 MET cc_start: 0.9653 (tmm) cc_final: 0.9238 (tmm)
REVERT: A  461 MET cc_start: 0.9172 (tpp) cc_final: 0.8915 (mmp)
REVERT: B   62 MET cc_start: 0.9114 (ttt) cc_final: 0.8633 (tpp)
REVERT: B  203 MET cc_start: 0.9550 (mmp) cc_final: 0.9068 (mmp)
REVERT: B  348 MET cc_start: 0.8791 (mmm) cc_final: 0.8355 (mtt)
REVERT: B  497 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9151 (pp)
  outliers start: 16
  outliers final: 12
  residues processed: 80
  average time/residue: 0.0834
  time to fit residues: 10.1054
Evaluate side-chains
  78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.058660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.040258 restraints weight = 44299.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 4.93
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9293  Z= 0.159
  Angle     :  0.661  11.365  12709  Z= 0.326
  Chirality :  0.042   0.239   1430
  Planarity :  0.003   0.049   1482
  Dihedral  : 18.193  78.209   1554
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.61 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1007
  helix:  1.52 (0.28), residues: 354
  sheet:  0.24 (0.40), residues: 160
  loop : -0.26 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M   9 
 TYR   0.008   0.001   TYR B 217 
 PHE   0.017   0.001   PHE A 227 
 TRP   0.004   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9292)
  covalent geometry    : angle       0.66089 (12709)
  hydrogen bonds       : bond        0.04316 (  403)
  hydrogen bonds       : angle       4.90927 ( 1092)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9465 (tpp) cc_final: 0.9171 (tpp)
REVERT: A  134 ILE cc_start: 0.8978 (mm) cc_final: 0.8584 (tt)
REVERT: A  427 MET cc_start: 0.9664 (tmm) cc_final: 0.9215 (tmm)
REVERT: A  461 MET cc_start: 0.9138 (tpp) cc_final: 0.8685 (mpp)
REVERT: B   62 MET cc_start: 0.9155 (ttt) cc_final: 0.8607 (tpp)
REVERT: B  203 MET cc_start: 0.9541 (mmp) cc_final: 0.9257 (mmp)
REVERT: B  348 MET cc_start: 0.8781 (mmm) cc_final: 0.8409 (mtt)
REVERT: B  462 MET cc_start: 0.8993 (ttp) cc_final: 0.8788 (ptp)
REVERT: B  497 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9153 (pp)
REVERT: M    9 ARG cc_start: 0.8943 (ptm-80) cc_final: 0.8663 (ptm-80)
  outliers start: 17
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0848
  time to fit residues: 9.6917
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0010
   chunk 81 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.059212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.040837 restraints weight = 44186.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 4.95
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9293  Z= 0.133
  Angle     :  0.666  11.344  12709  Z= 0.324
  Chirality :  0.042   0.241   1430
  Planarity :  0.003   0.046   1482
  Dihedral  : 18.116  75.001   1554
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.16 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1007
  helix:  1.48 (0.28), residues: 355
  sheet:  0.30 (0.40), residues: 160
  loop : -0.19 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M   9 
 TYR   0.009   0.001   TYR B 217 
 PHE   0.019   0.001   PHE A 227 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9292)
  covalent geometry    : angle       0.66641 (12709)
  hydrogen bonds       : bond        0.04004 (  403)
  hydrogen bonds       : angle       4.88004 ( 1092)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 ILE cc_start: 0.9025 (mm) cc_final: 0.8638 (tt)
REVERT: A  427 MET cc_start: 0.9658 (tmm) cc_final: 0.9221 (tmm)
REVERT: A  461 MET cc_start: 0.9163 (tpp) cc_final: 0.8682 (mmp)
REVERT: B   62 MET cc_start: 0.9132 (ttt) cc_final: 0.8585 (tpp)
REVERT: B  203 MET cc_start: 0.9546 (mmp) cc_final: 0.9276 (mmp)
REVERT: B  348 MET cc_start: 0.8732 (mmm) cc_final: 0.8366 (mtt)
REVERT: B  497 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9157 (pp)
  outliers start: 13
  outliers final: 11
  residues processed: 76
  average time/residue: 0.0927
  time to fit residues: 10.3308
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0980
   chunk 48 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 86 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.6362

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.060022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.041642 restraints weight = 43563.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 5.02
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9293  Z= 0.116
  Angle     :  0.685  16.299  12709  Z= 0.327
  Chirality :  0.042   0.293   1430
  Planarity :  0.003   0.045   1482
  Dihedral  : 18.042  71.633   1554
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.70 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.27), residues: 1007
  helix:  1.52 (0.28), residues: 354
  sheet:  0.27 (0.40), residues: 159
  loop : -0.15 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M   9 
 TYR   0.008   0.001   TYR A 264 
 PHE   0.023   0.001   PHE A 227 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.002   0.000   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9292)
  covalent geometry    : angle       0.68518 (12709)
  hydrogen bonds       : bond        0.03862 (  403)
  hydrogen bonds       : angle       4.85952 ( 1092)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1727.57 seconds
wall clock time: 30 minutes 36.33 seconds (1836.33 seconds total)