Starting phenix.real_space_refine
on Tue Mar  3 23:56:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvc_4647/03_2026/6qvc_4647.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvc_4647/03_2026/6qvc_4647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvc_4647/03_2026/6qvc_4647.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvc_4647/03_2026/6qvc_4647.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qvc_4647/03_2026/6qvc_4647.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvc_4647/03_2026/6qvc_4647.map"
  }
  resolution = 4.0
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    6132      2.51       5
     N    1484      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9272
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 4636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 599, 4636
          Classifications: {'peptide': 599}
          Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569}
          Chain breaks: 3
  Restraints were copied for chains:
    A
  Time building chain proxies: 3.61, per 1000 atoms: 0.39
  Number of scatterers: 9272
  At special positions: 0
  Unit cell: (105.93, 103.79, 109.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    1586      8.00
     N    1484      7.00
     C    6132      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=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 361.7 milliseconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2216

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      66.4% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 116 through 153
    Processing helix  chain 'B' and resid 158 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 4.413A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 208 through 225
      removed outlier: 3.627A  pdb=" N   PHE B 212 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.611A  pdb=" N   PHE B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 280
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 324
      removed outlier: 3.549A  pdb=" N   ARG B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 377
      removed outlier: 4.151A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
    Processing helix  chain 'B' and resid 391 through 403
      removed outlier: 4.691A  pdb=" N   GLY B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL B 397 " --> pdb=" O   TYR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.516A  pdb=" N   ILE B 450 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 3.530A  pdb=" N   ILE B 459 " --> pdb=" O   ASN B 455 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE B 472 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   MET B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 538
      removed outlier: 4.539A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.948A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
    Processing helix  chain 'B' and resid 576 through 586
    Processing helix  chain 'B' and resid 621 through 632
    Processing helix  chain 'B' and resid 654 through 666
    Processing helix  chain 'B' and resid 833 through 845
    Processing helix  chain 'B' and resid 862 through 871
    Processing helix  chain 'A' and resid 116 through 153
    Processing helix  chain 'A' and resid 158 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 4.413A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 3.626A  pdb=" N   PHE A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.610A  pdb=" N   PHE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 280
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 324
      removed outlier: 3.550A  pdb=" N   ARG A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 377
      removed outlier: 4.151A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
    Processing helix  chain 'A' and resid 391 through 403
      removed outlier: 4.691A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL A 397 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.516A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 3.530A  pdb=" N   ILE A 459 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE A 472 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   MET A 477 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 4.538A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 3.949A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
    Processing helix  chain 'A' and resid 576 through 586
    Processing helix  chain 'A' and resid 621 through 632
    Processing helix  chain 'A' and resid 654 through 666
    Processing helix  chain 'A' and resid 833 through 845
    Processing helix  chain 'A' and resid 862 through 871
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'B' and resid 616 through 617
      removed outlier: 6.096A  pdb=" N   VAL B 616 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP B 822 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853
      removed outlier: 6.582A  pdb=" N   ALA B 849 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL B 860 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B 851 " --> pdb=" O   ARG B 858 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 617
      removed outlier: 6.096A  pdb=" N   VAL A 616 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP A 822 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853
      removed outlier: 6.581A  pdb=" N   ALA A 849 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL A 860 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)

    586 hydrogen bonds defined for protein.
    1710 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: 1.37

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2748
        1.34 -     1.46: 2200
        1.46 -     1.58: 4440
        1.58 -     1.70: 0
        1.70 -     1.82: 116
  Bond restraints: 9504
  Sorted by residual:
  bond pdb=" CG1 ILE B 527 "
       pdb=" CD1 ILE B 527 "
    ideal  model  delta    sigma   weight residual
    1.513  1.389  0.124 3.90e-02 6.57e+02 1.02e+01
  bond pdb=" CG1 ILE A 527 "
       pdb=" CD1 ILE A 527 "
    ideal  model  delta    sigma   weight residual
    1.513  1.389  0.124 3.90e-02 6.57e+02 1.01e+01
  bond pdb=" CB  ILE A 354 "
       pdb=" CG2 ILE A 354 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.68e+00
  bond pdb=" CB  ILE B 354 "
       pdb=" CG2 ILE B 354 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.63e+00
  bond pdb=" C   PHE A 343 "
       pdb=" N   ASP A 344 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.40e-02 5.10e+03 5.68e+00
  ... (remaining 9499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 12606
        4.15 -     8.29: 262
        8.29 -    12.44: 36
       12.44 -    16.59: 8
       16.59 -    20.73: 2
  Bond angle restraints: 12914
  Sorted by residual:
  angle pdb=" C   PHE A 343 "
        pdb=" N   ASP A 344 "
        pdb=" CA  ASP A 344 "
      ideal   model   delta    sigma   weight residual
     121.70  132.56  -10.86 1.80e+00 3.09e-01 3.64e+01
  angle pdb=" C   PHE B 343 "
        pdb=" N   ASP B 344 "
        pdb=" CA  ASP B 344 "
      ideal   model   delta    sigma   weight residual
     121.70  132.48  -10.78 1.80e+00 3.09e-01 3.59e+01
  angle pdb=" CA  LEU A 171 "
        pdb=" CB  LEU A 171 "
        pdb=" CG  LEU A 171 "
      ideal   model   delta    sigma   weight residual
     116.30  137.03  -20.73 3.50e+00 8.16e-02 3.51e+01
  angle pdb=" CA  LEU B 171 "
        pdb=" CB  LEU B 171 "
        pdb=" CG  LEU B 171 "
      ideal   model   delta    sigma   weight residual
     116.30  136.99  -20.69 3.50e+00 8.16e-02 3.49e+01
  angle pdb=" C   THR B 621 "
        pdb=" N   TYR B 622 "
        pdb=" CA  TYR B 622 "
      ideal   model   delta    sigma   weight residual
     120.82  128.30   -7.48 1.50e+00 4.44e-01 2.49e+01
  ... (remaining 12909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.08: 4989
       14.08 -    28.16: 433
       28.16 -    42.24: 108
       42.24 -    56.32: 20
       56.32 -    70.40: 6
  Dihedral angle restraints: 5556
    sinusoidal: 2114
      harmonic: 3442
  Sorted by residual:
  dihedral pdb=" CA  ALA A 326 "
           pdb=" C   ALA A 326 "
           pdb=" N   VAL A 327 "
           pdb=" CA  VAL A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.06  -44.94     0      5.00e+00 4.00e-02 8.08e+01
  dihedral pdb=" CA  ALA B 326 "
           pdb=" C   ALA B 326 "
           pdb=" N   VAL B 327 "
           pdb=" CA  VAL B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.14  -44.86     0      5.00e+00 4.00e-02 8.05e+01
  dihedral pdb=" CA  ILE B 290 "
           pdb=" C   ILE B 290 "
           pdb=" N   GLU B 291 "
           pdb=" CA  GLU B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.15  -34.85     0      5.00e+00 4.00e-02 4.86e+01
  ... (remaining 5553 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1322
       0.112 -    0.225: 171
       0.225 -    0.337: 31
       0.337 -    0.450: 0
       0.450 -    0.562: 2
  Chirality restraints: 1526
  Sorted by residual:
  chirality pdb=" CB  VAL B 321 "
            pdb=" CA  VAL B 321 "
            pdb=" CG1 VAL B 321 "
            pdb=" CG2 VAL B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.90e+00
  chirality pdb=" CB  VAL A 321 "
            pdb=" CA  VAL A 321 "
            pdb=" CG1 VAL A 321 "
            pdb=" CG2 VAL A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.84e+00
  chirality pdb=" CB  ILE B 329 "
            pdb=" CA  ILE B 329 "
            pdb=" CG1 ILE B 329 "
            pdb=" CG2 ILE B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.95   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1523 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 469 "    0.035 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP B 469 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 469 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 469 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 469 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 469 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 469 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 469 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 469 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 469 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 469 "   -0.035 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP A 469 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 469 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 469 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 469 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 469 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 469 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 469 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 469 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 469 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 327 "    0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   VAL A 327 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   VAL A 327 "    0.021 2.00e-02 2.50e+03
        pdb=" N   THR A 328 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1622
        2.77 -     3.30: 9375
        3.30 -     3.83: 15743
        3.83 -     4.37: 17403
        4.37 -     4.90: 28449
  Nonbonded interactions: 72592
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 472 "
            pdb=" OG1 THR A 476 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ILE B 472 "
            pdb=" OG1 THR B 476 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ILE B 401 "
            pdb=" OG1 THR B 405 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE A 401 "
            pdb=" OG1 THR A 405 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR B 632 "
            pdb=" NH1 ARG B 654 "
     model   vdw
     2.249 3.120
  ... (remaining 72587 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.920
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
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      :  0.008   0.124   9504  Z= 0.351
  Angle     :  1.474  20.735  12914  Z= 0.771
  Chirality :  0.080   0.562   1526
  Planarity :  0.010   0.059   1580
  Dihedral  : 11.978  70.398   3340
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.38 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  8.95 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.71 %

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 are not related in a simple way.
  whole: -3.90 (0.20), residues: 1182
  helix: -2.23 (0.15), residues: 758
  sheet: -0.42 (0.90), residues: 20
  loop : -3.15 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 626 
 TYR   0.031   0.003   TYR B 589 
 PHE   0.037   0.004   PHE A 547 
 TRP   0.053   0.005   TRP A 469 
 HIS   0.008   0.002   HIS A 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00827 ( 9504)
  covalent geometry    : angle       1.47378 (12914)
  hydrogen bonds       : bond        0.16440 (  586)
  hydrogen bonds       : angle       7.15464 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 225
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  126 LEU cc_start: 0.9707 (tt) cc_final: 0.9436 (pp)
REVERT: B  128 MET cc_start: 0.9329 (tpp) cc_final: 0.8925 (tpp)
REVERT: B  194 MET cc_start: 0.8984 (ppp) cc_final: 0.8701 (ppp)
REVERT: B  277 CYS cc_start: 0.8164 (t) cc_final: 0.7577 (t)
REVERT: B  301 ASN cc_start: 0.8804 (m-40) cc_final: 0.8438 (m-40)
REVERT: B  302 TYR cc_start: 0.9326 (t80) cc_final: 0.9019 (t80)
REVERT: B  307 PHE cc_start: 0.8795 (t80) cc_final: 0.8593 (t80)
REVERT: B  323 ASN cc_start: 0.8838 (m-40) cc_final: 0.8171 (m-40)
REVERT: B  385 PHE cc_start: 0.8736 (t80) cc_final: 0.8529 (m-80)
REVERT: B  432 THR cc_start: 0.9306 (m) cc_final: 0.9076 (p)
REVERT: B  472 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8958 (mt)
REVERT: B  614 LYS cc_start: 0.9531 (pmtt) cc_final: 0.9306 (tptp)
REVERT: B  865 GLU cc_start: 0.9364 (mp0) cc_final: 0.9075 (mp0)
REVERT: B  868 LYS cc_start: 0.9471 (mttt) cc_final: 0.9236 (mttt)
REVERT: A  126 LEU cc_start: 0.9734 (tt) cc_final: 0.9444 (pp)
REVERT: A  128 MET cc_start: 0.9410 (tpp) cc_final: 0.8866 (tpp)
REVERT: A  173 LEU cc_start: 0.8987 (pp) cc_final: 0.8770 (pp)
REVERT: A  194 MET cc_start: 0.8837 (ppp) cc_final: 0.8488 (ppp)
REVERT: A  250 MET cc_start: 0.9139 (tpt) cc_final: 0.8934 (tpp)
REVERT: A  277 CYS cc_start: 0.7868 (t) cc_final: 0.7227 (t)
REVERT: A  301 ASN cc_start: 0.8730 (m-40) cc_final: 0.8331 (m-40)
REVERT: A  302 TYR cc_start: 0.9336 (t80) cc_final: 0.9006 (t80)
REVERT: A  323 ASN cc_start: 0.8910 (m-40) cc_final: 0.8262 (m-40)
REVERT: A  432 THR cc_start: 0.9388 (m) cc_final: 0.9104 (p)
REVERT: A  466 MET cc_start: 0.8711 (tpt) cc_final: 0.8471 (tpt)
REVERT: A  472 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8957 (tt)
REVERT: A  868 LYS cc_start: 0.9536 (mttt) cc_final: 0.9302 (mttm)
  outliers start: 22
  outliers final: 1
  residues processed: 234
  average time/residue: 0.0947
  time to fit residues: 30.9786
Evaluate side-chains
  134 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  472 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 117 optimal weight:    6.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 658 GLN
A 384 GLN
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 658 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.074846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.054908 restraints weight = 40547.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.056559 restraints weight = 23484.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.057815 restraints weight = 15842.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.058389 restraints weight = 11816.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.059045 restraints weight = 9868.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9504  Z= 0.216
  Angle     :  0.933  12.344  12914  Z= 0.463
  Chirality :  0.047   0.183   1526
  Planarity :  0.006   0.045   1580
  Dihedral  :  7.004  47.267   1268
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.40 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -1.52 (0.24), residues: 1182
  helix: -0.13 (0.18), residues: 776
  sheet: -0.33 (0.96), residues: 20
  loop : -2.84 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 611 
 TYR   0.013   0.001   TYR B 620 
 PHE   0.039   0.002   PHE A 547 
 TRP   0.027   0.002   TRP A 469 
 HIS   0.009   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 9504)
  covalent geometry    : angle       0.93253 (12914)
  hydrogen bonds       : bond        0.05569 (  586)
  hydrogen bonds       : angle       5.06179 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9181 (tpp) cc_final: 0.8919 (tpp)
REVERT: B  194 MET cc_start: 0.8826 (ppp) cc_final: 0.8518 (ppp)
REVERT: B  277 CYS cc_start: 0.8095 (t) cc_final: 0.7854 (t)
REVERT: B  302 TYR cc_start: 0.9483 (t80) cc_final: 0.9068 (t80)
REVERT: B  391 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8356 (tp)
REVERT: B  826 PHE cc_start: 0.6914 (p90) cc_final: 0.6658 (p90)
REVERT: A  128 MET cc_start: 0.9239 (tpp) cc_final: 0.8912 (tpp)
REVERT: A  194 MET cc_start: 0.8682 (ppp) cc_final: 0.8386 (ppp)
REVERT: A  277 CYS cc_start: 0.7983 (t) cc_final: 0.7740 (t)
REVERT: A  302 TYR cc_start: 0.9478 (t80) cc_final: 0.9112 (t80)
REVERT: A  391 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8687 (tp)
REVERT: A  466 MET cc_start: 0.8660 (tpt) cc_final: 0.8112 (tpp)
REVERT: A  470 MET cc_start: 0.8465 (mmm) cc_final: 0.7649 (mmm)
REVERT: A  504 MET cc_start: 0.9033 (tmm) cc_final: 0.8770 (ppp)
REVERT: A  868 LYS cc_start: 0.9571 (mttt) cc_final: 0.9363 (mttt)
  outliers start: 37
  outliers final: 12
  residues processed: 178
  average time/residue: 0.0745
  time to fit residues: 20.3237
Evaluate side-chains
  132 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 451 HIS
A 160 GLN
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.076356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.055956 restraints weight = 40451.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057765 restraints weight = 22850.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.059026 restraints weight = 15271.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.059881 restraints weight = 11315.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.060390 restraints weight = 9179.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9504  Z= 0.153
  Angle     :  0.894  14.027  12914  Z= 0.422
  Chirality :  0.047   0.209   1526
  Planarity :  0.005   0.053   1580
  Dihedral  :  6.384  54.335   1266
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.79 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole: -0.55 (0.25), residues: 1182
  helix:  0.76 (0.19), residues: 758
  sheet: -0.24 (0.97), residues: 20
  loop : -2.62 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 669 
 TYR   0.011   0.001   TYR A 137 
 PHE   0.037   0.002   PHE A 547 
 TRP   0.022   0.002   TRP B 469 
 HIS   0.006   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9504)
  covalent geometry    : angle       0.89417 (12914)
  hydrogen bonds       : bond        0.04800 (  586)
  hydrogen bonds       : angle       4.67280 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 148
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9180 (tpp) cc_final: 0.8860 (tpp)
REVERT: B  194 MET cc_start: 0.8839 (ppp) cc_final: 0.8528 (ppp)
REVERT: B  302 TYR cc_start: 0.9506 (t80) cc_final: 0.9086 (t80)
REVERT: B  466 MET cc_start: 0.8982 (mmp) cc_final: 0.8603 (mmm)
REVERT: B  470 MET cc_start: 0.8526 (mmm) cc_final: 0.8316 (mmm)
REVERT: B  504 MET cc_start: 0.8850 (tmm) cc_final: 0.8646 (ppp)
REVERT: B  826 PHE cc_start: 0.6666 (p90) cc_final: 0.6351 (p90)
REVERT: B  868 LYS cc_start: 0.9399 (mttm) cc_final: 0.9067 (mtmm)
REVERT: A  128 MET cc_start: 0.9193 (tpp) cc_final: 0.8876 (tpp)
REVERT: A  160 GLN cc_start: 0.9092 (mt0) cc_final: 0.8673 (mp10)
REVERT: A  194 MET cc_start: 0.8689 (ppp) cc_final: 0.8322 (ppp)
REVERT: A  302 TYR cc_start: 0.9485 (t80) cc_final: 0.9106 (t80)
REVERT: A  391 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8764 (tp)
REVERT: A  466 MET cc_start: 0.8654 (tpt) cc_final: 0.8107 (tpp)
REVERT: A  470 MET cc_start: 0.8566 (mmm) cc_final: 0.7608 (mmm)
REVERT: A  472 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9020 (tt)
  outliers start: 44
  outliers final: 15
  residues processed: 179
  average time/residue: 0.0737
  time to fit residues: 20.2692
Evaluate side-chains
  138 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:   30.0000
   chunk 31 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.7958

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

Flipped N/Q/H residues before XYZ refinement:
B 323 ASN
A 323 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.076260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.056286 restraints weight = 40403.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.058037 restraints weight = 23190.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.059073 restraints weight = 15682.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.059992 restraints weight = 12276.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060653 restraints weight = 9762.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9504  Z= 0.144
  Angle     :  0.864  12.898  12914  Z= 0.402
  Chirality :  0.046   0.219   1526
  Planarity :  0.005   0.052   1580
  Dihedral  :  5.712  39.558   1264
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.18 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole: -0.21 (0.25), residues: 1182
  helix:  1.02 (0.19), residues: 760
  sheet: -0.11 (0.97), residues: 20
  loop : -2.48 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 669 
 TYR   0.011   0.001   TYR A 137 
 PHE   0.034   0.002   PHE A 547 
 TRP   0.017   0.002   TRP B 469 
 HIS   0.005   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9504)
  covalent geometry    : angle       0.86400 (12914)
  hydrogen bonds       : bond        0.04470 (  586)
  hydrogen bonds       : angle       4.46465 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 143
  time to evaluate  : 0.283 
Fit side-chains
REVERT: B  194 MET cc_start: 0.8749 (ppp) cc_final: 0.8407 (ppp)
REVERT: B  302 TYR cc_start: 0.9425 (t80) cc_final: 0.9034 (t80)
REVERT: B  391 LEU cc_start: 0.8905 (tt) cc_final: 0.8483 (tp)
REVERT: B  466 MET cc_start: 0.8862 (mmp) cc_final: 0.8593 (mmp)
REVERT: A  153 MET cc_start: 0.8657 (ppp) cc_final: 0.8337 (ppp)
REVERT: A  194 MET cc_start: 0.8632 (ppp) cc_final: 0.8282 (ppp)
REVERT: A  302 TYR cc_start: 0.9439 (t80) cc_final: 0.9042 (t80)
REVERT: A  391 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8717 (tp)
REVERT: A  466 MET cc_start: 0.8577 (tpt) cc_final: 0.8128 (tpp)
REVERT: A  470 MET cc_start: 0.8539 (mmm) cc_final: 0.7579 (mmm)
REVERT: A  826 PHE cc_start: 0.6547 (p90) cc_final: 0.6199 (p90)
REVERT: A  865 GLU cc_start: 0.9698 (mp0) cc_final: 0.9319 (mp0)
REVERT: A  868 LYS cc_start: 0.9579 (mttt) cc_final: 0.9350 (mttt)
  outliers start: 41
  outliers final: 25
  residues processed: 171
  average time/residue: 0.0687
  time to fit residues: 18.2211
Evaluate side-chains
  154 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain B residue  609 MET
Chi-restraints excluded: chain B residue  615 PHE
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 436 HIS
A 436 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.074133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.053742 restraints weight = 41228.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055448 restraints weight = 23661.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.056709 restraints weight = 16014.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057541 restraints weight = 11926.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.058026 restraints weight = 9660.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.4671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9504  Z= 0.198
  Angle     :  0.893  14.563  12914  Z= 0.425
  Chirality :  0.047   0.216   1526
  Planarity :  0.005   0.052   1580
  Dihedral  :  5.657  43.338   1264
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.97 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole: -0.08 (0.25), residues: 1182
  helix:  1.18 (0.19), residues: 754
  sheet: -0.11 (0.97), residues: 20
  loop : -2.52 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 334 
 TYR   0.011   0.001   TYR B 146 
 PHE   0.031   0.002   PHE A 547 
 TRP   0.015   0.002   TRP B 469 
 HIS   0.005   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 9504)
  covalent geometry    : angle       0.89297 (12914)
  hydrogen bonds       : bond        0.04801 (  586)
  hydrogen bonds       : angle       4.66389 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 132
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  153 MET cc_start: 0.8721 (ppp) cc_final: 0.8398 (ppp)
REVERT: B  194 MET cc_start: 0.8799 (ppp) cc_final: 0.8426 (ppp)
REVERT: B  302 TYR cc_start: 0.9514 (t80) cc_final: 0.9049 (t80)
REVERT: B  391 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8426 (tp)
REVERT: B  826 PHE cc_start: 0.6749 (p90) cc_final: 0.6437 (p90)
REVERT: A  194 MET cc_start: 0.8684 (ppp) cc_final: 0.8297 (ppp)
REVERT: A  302 TYR cc_start: 0.9510 (t80) cc_final: 0.9079 (t80)
REVERT: A  391 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8744 (tp)
REVERT: A  466 MET cc_start: 0.8626 (tpt) cc_final: 0.8286 (tpp)
REVERT: A  470 MET cc_start: 0.8632 (mmm) cc_final: 0.8065 (mmm)
  outliers start: 51
  outliers final: 32
  residues processed: 167
  average time/residue: 0.0659
  time to fit residues: 17.3644
Evaluate side-chains
  153 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  563 VAL
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 103 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 838 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.076059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.055764 restraints weight = 40708.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.057476 restraints weight = 23576.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.058696 restraints weight = 16034.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.059327 restraints weight = 11993.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.060013 restraints weight = 9991.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9504  Z= 0.152
  Angle     :  0.925  14.251  12914  Z= 0.425
  Chirality :  0.048   0.215   1526
  Planarity :  0.005   0.050   1580
  Dihedral  :  5.517  43.848   1264
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.76 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.17 (0.25), residues: 1182
  helix:  1.38 (0.19), residues: 752
  sheet: -0.26 (0.98), residues: 20
  loop : -2.38 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.010   0.001   TYR A 137 
 PHE   0.033   0.001   PHE A 547 
 TRP   0.015   0.001   TRP B 469 
 HIS   0.007   0.001   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9504)
  covalent geometry    : angle       0.92491 (12914)
  hydrogen bonds       : bond        0.04595 (  586)
  hydrogen bonds       : angle       4.45512 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 140
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  194 MET cc_start: 0.8683 (ppp) cc_final: 0.8481 (ppp)
REVERT: B  302 TYR cc_start: 0.9403 (t80) cc_final: 0.9031 (t80)
REVERT: B  391 LEU cc_start: 0.8883 (tt) cc_final: 0.8455 (tp)
REVERT: A  178 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8402 (m-80)
REVERT: A  194 MET cc_start: 0.8599 (ppp) cc_final: 0.8368 (ppp)
REVERT: A  302 TYR cc_start: 0.9421 (t80) cc_final: 0.9011 (t80)
REVERT: A  391 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8701 (tp)
REVERT: A  470 MET cc_start: 0.8691 (mmm) cc_final: 0.8320 (mmm)
REVERT: A  646 MET cc_start: 0.7946 (ppp) cc_final: 0.7737 (ppp)
REVERT: A  826 PHE cc_start: 0.6609 (p90) cc_final: 0.6262 (p90)
  outliers start: 40
  outliers final: 30
  residues processed: 166
  average time/residue: 0.0685
  time to fit residues: 17.9543
Evaluate side-chains
  157 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain B residue  838 HIS
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  323 ASN
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  838 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** B 838 HIS ** 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 = 0.3452 r_free = 0.3452 target = 0.075632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.055518 restraints weight = 40433.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.057228 restraints weight = 23599.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.058377 restraints weight = 16049.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.059124 restraints weight = 12143.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.059569 restraints weight = 9950.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.5095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9504  Z= 0.167
  Angle     :  0.954  16.739  12914  Z= 0.437
  Chirality :  0.048   0.213   1526
  Planarity :  0.005   0.074   1580
  Dihedral  :  5.459  44.431   1264
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.17 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.12 (0.25), residues: 1182
  helix:  1.33 (0.19), residues: 750
  sheet: -0.28 (1.00), residues: 20
  loop : -2.38 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.010   0.001   TYR B 146 
 PHE   0.032   0.001   PHE B 547 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.006   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9504)
  covalent geometry    : angle       0.95380 (12914)
  hydrogen bonds       : bond        0.04702 (  586)
  hydrogen bonds       : angle       4.48726 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8613 (m-80)
REVERT: B  194 MET cc_start: 0.8725 (ppp) cc_final: 0.8476 (ppp)
REVERT: B  302 TYR cc_start: 0.9439 (t80) cc_final: 0.8996 (t80)
REVERT: B  391 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8383 (tp)
REVERT: B  826 PHE cc_start: 0.6666 (p90) cc_final: 0.6395 (p90)
REVERT: A  178 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8443 (m-80)
REVERT: A  194 MET cc_start: 0.8656 (ppp) cc_final: 0.8385 (ppp)
REVERT: A  302 TYR cc_start: 0.9417 (t80) cc_final: 0.9015 (t80)
REVERT: A  391 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8671 (tp)
REVERT: A  854 MET cc_start: 0.8271 (tmm) cc_final: 0.8044 (tmm)
  outliers start: 38
  outliers final: 27
  residues processed: 155
  average time/residue: 0.0678
  time to fit residues: 16.6961
Evaluate side-chains
  156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain B residue  838 HIS
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  568 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 70 optimal weight:    0.3980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 323 ASN
B 369 HIS
** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.076109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.055921 restraints weight = 40445.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.057679 restraints weight = 23559.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.058679 restraints weight = 15958.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.059614 restraints weight = 12417.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.060008 restraints weight = 10017.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.5274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9504  Z= 0.152
  Angle     :  0.977  15.327  12914  Z= 0.440
  Chirality :  0.048   0.291   1526
  Planarity :  0.005   0.066   1580
  Dihedral  :  5.361  44.698   1264
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.96 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.21 (0.25), residues: 1182
  helix:  1.43 (0.19), residues: 750
  sheet: -0.26 (1.02), residues: 20
  loop : -2.40 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 370 
 TYR   0.010   0.001   TYR A 137 
 PHE   0.033   0.001   PHE A 547 
 TRP   0.015   0.001   TRP B 469 
 HIS   0.020   0.001   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9504)
  covalent geometry    : angle       0.97666 (12914)
  hydrogen bonds       : bond        0.04526 (  586)
  hydrogen bonds       : angle       4.46328 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8595 (m-80)
REVERT: B  302 TYR cc_start: 0.9406 (t80) cc_final: 0.9021 (t80)
REVERT: B  826 PHE cc_start: 0.6797 (p90) cc_final: 0.6491 (p90)
REVERT: A  178 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8506 (m-80)
REVERT: A  194 MET cc_start: 0.8593 (ppp) cc_final: 0.8391 (ppp)
REVERT: A  302 TYR cc_start: 0.9398 (t80) cc_final: 0.9015 (t80)
REVERT: A  391 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8650 (tp)
REVERT: A  487 VAL cc_start: 0.9603 (OUTLIER) cc_final: 0.9391 (p)
REVERT: A  548 GLU cc_start: 0.8893 (pt0) cc_final: 0.8678 (pp20)
REVERT: A  826 PHE cc_start: 0.6492 (p90) cc_final: 0.6211 (p90)
  outliers start: 38
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0660
  time to fit residues: 16.7218
Evaluate side-chains
  159 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  568 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 369 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.075403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.055525 restraints weight = 40476.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.057214 restraints weight = 23550.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.058212 restraints weight = 16112.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.059138 restraints weight = 12644.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.059601 restraints weight = 10191.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.5413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9504  Z= 0.156
  Angle     :  1.030  16.754  12914  Z= 0.460
  Chirality :  0.049   0.284   1526
  Planarity :  0.005   0.063   1580
  Dihedral  :  5.347  45.421   1264
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.16 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.23 (0.25), residues: 1182
  helix:  1.44 (0.19), residues: 750
  sheet: -0.26 (1.03), residues: 20
  loop : -2.38 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 611 
 TYR   0.009   0.001   TYR A 137 
 PHE   0.032   0.001   PHE B 547 
 TRP   0.016   0.001   TRP A 469 
 HIS   0.007   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9504)
  covalent geometry    : angle       1.02982 (12914)
  hydrogen bonds       : bond        0.04506 (  586)
  hydrogen bonds       : angle       4.44860 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 136
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  302 TYR cc_start: 0.9423 (t80) cc_final: 0.9005 (t80)
REVERT: B  826 PHE cc_start: 0.6681 (p90) cc_final: 0.6339 (p90)
REVERT: A  178 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8583 (m-80)
REVERT: A  302 TYR cc_start: 0.9420 (t80) cc_final: 0.9049 (t80)
REVERT: A  391 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8586 (tp)
REVERT: A  470 MET cc_start: 0.8411 (mmm) cc_final: 0.8188 (mmm)
REVERT: A  487 VAL cc_start: 0.9594 (OUTLIER) cc_final: 0.9386 (p)
REVERT: A  548 GLU cc_start: 0.8887 (pt0) cc_final: 0.8638 (pp20)
  outliers start: 39
  outliers final: 28
  residues processed: 160
  average time/residue: 0.0659
  time to fit residues: 16.7863
Evaluate side-chains
  160 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  563 VAL
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  568 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 103 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.075733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.055965 restraints weight = 40392.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.057562 restraints weight = 23551.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.058833 restraints weight = 16204.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.059538 restraints weight = 12046.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060218 restraints weight = 9960.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.5544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9504  Z= 0.153
  Angle     :  1.039  15.048  12914  Z= 0.463
  Chirality :  0.049   0.330   1526
  Planarity :  0.005   0.062   1580
  Dihedral  :  5.287  45.449   1264
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.65 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.26 (0.25), residues: 1182
  helix:  1.46 (0.19), residues: 750
  sheet: -0.17 (1.03), residues: 20
  loop : -2.34 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 334 
 TYR   0.008   0.001   TYR B 146 
 PHE   0.032   0.001   PHE B 547 
 TRP   0.015   0.001   TRP A 469 
 HIS   0.010   0.001   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9504)
  covalent geometry    : angle       1.03866 (12914)
  hydrogen bonds       : bond        0.04464 (  586)
  hydrogen bonds       : angle       4.44529 ( 1710)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  302 TYR cc_start: 0.9416 (t80) cc_final: 0.9044 (t80)
REVERT: B  826 PHE cc_start: 0.6493 (p90) cc_final: 0.6174 (p90)
REVERT: A  178 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8641 (m-80)
REVERT: A  302 TYR cc_start: 0.9423 (t80) cc_final: 0.9060 (t80)
REVERT: A  391 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8592 (tp)
REVERT: A  504 MET cc_start: 0.9108 (ppp) cc_final: 0.8874 (ppp)
REVERT: A  826 PHE cc_start: 0.6603 (p90) cc_final: 0.6319 (p90)
  outliers start: 32
  outliers final: 26
  residues processed: 165
  average time/residue: 0.0673
  time to fit residues: 17.4884
Evaluate side-chains
  168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  563 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  568 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0670
   chunk 29 optimal weight:    0.0050
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.5532

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.076764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.056985 restraints weight = 40072.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.058698 restraints weight = 23500.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.059692 restraints weight = 16104.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.060632 restraints weight = 12529.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.061291 restraints weight = 10031.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.5708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9504  Z= 0.152
  Angle     :  1.040  14.592  12914  Z= 0.461
  Chirality :  0.049   0.318   1526
  Planarity :  0.005   0.062   1580
  Dihedral  :  5.201  45.635   1264
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.75 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.31 (0.26), residues: 1182
  helix:  1.46 (0.19), residues: 750
  sheet: -0.06 (1.03), residues: 20
  loop : -2.26 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 334 
 TYR   0.008   0.001   TYR B 524 
 PHE   0.033   0.001   PHE B 547 
 TRP   0.019   0.001   TRP A 469 
 HIS   0.008   0.001   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9504)
  covalent geometry    : angle       1.03959 (12914)
  hydrogen bonds       : bond        0.04353 (  586)
  hydrogen bonds       : angle       4.50976 ( 1710)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1447.71 seconds
wall clock time: 25 minutes 51.27 seconds (1551.27 seconds total)