Starting phenix.real_space_refine
on Tue Mar  3 23:56:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvu_4657/03_2026/6qvu_4657.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvu_4657/03_2026/6qvu_4657.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qvu_4657/03_2026/6qvu_4657.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvu_4657/03_2026/6qvu_4657.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvu_4657/03_2026/6qvu_4657.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvu_4657/03_2026/6qvu_4657.cif"
  }
  resolution = 4.2
  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 28 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: 2.98, per 1000 atoms: 0.32
  Number of scatterers: 9272
  At special positions: 0
  Unit cell: (105.93, 102.72, 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: 0.56
  Conformation dependent library (CDL) restraints added in 258.5 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:
      46 helices and 6 sheets defined
      64.7% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 115 through 153
    Processing helix  chain 'B' and resid 156 through 181
      removed outlier: 3.522A  pdb=" N   PHE B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 191 through 198
    Processing helix  chain 'B' and resid 208 through 224
      removed outlier: 3.514A  pdb=" N   ALA B 214 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
    Processing helix  chain 'B' and resid 263 through 279
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 323
      removed outlier: 3.673A  pdb=" N   TYR B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU B 319 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   VAL B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 377
      removed outlier: 3.912A  pdb=" N   ALA B 353 " --> pdb=" O   PRO B 349 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   CYS B 357 " --> pdb=" O   ALA B 353 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 389
    Processing helix  chain 'B' and resid 392 through 403
      removed outlier: 3.591A  pdb=" N   ILE B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 4.021A  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: 3.804A  pdb=" N   ILE B 450 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 3.804A  pdb=" N   ILE B 472 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
      removed outlier: 3.824A  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: 5.213A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.620A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY B 551 " --> pdb=" O   PHE B 547 " (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
      removed outlier: 3.747A  pdb=" N   THR B 632 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
    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 872
      removed outlier: 4.024A  pdb=" N   GLY B 872 " --> pdb=" O   LYS B 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 153
    Processing helix  chain 'A' and resid 156 through 181
      removed outlier: 3.521A  pdb=" N   PHE A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 191 through 198
    Processing helix  chain 'A' and resid 208 through 224
      removed outlier: 3.515A  pdb=" N   ALA A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
    Processing helix  chain 'A' and resid 263 through 279
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 323
      removed outlier: 3.673A  pdb=" N   TYR A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 319 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   VAL A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 377
      removed outlier: 3.910A  pdb=" N   ALA A 353 " --> pdb=" O   PRO A 349 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY A 355 " --> pdb=" O   PHE A 351 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   CYS A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 389
    Processing helix  chain 'A' and resid 392 through 403
      removed outlier: 3.590A  pdb=" N   ILE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 4.022A  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: 3.804A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 3.803A  pdb=" N   ILE A 472 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
      removed outlier: 3.824A  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: 5.213A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 3.620A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY A 551 " --> pdb=" O   PHE A 547 " (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
      removed outlier: 3.748A  pdb=" N   THR A 632 " --> pdb=" O   LEU A 628 " (cutoff:3.500A)
    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 872
      removed outlier: 4.025A  pdb=" N   GLY A 872 " --> pdb=" O   LYS A 868 " (cutoff:3.500A)
    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: 5.567A  pdb=" N   VAL B 616 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   LEU B 637 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   SER B 651 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU B 639 " --> pdb=" O   LEU B 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853
      removed outlier: 6.458A  pdb=" N   ALA B 849 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   VAL B 860 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
      removed outlier: 6.677A  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: 5.567A  pdb=" N   VAL A 616 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   LEU A 637 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   SER A 651 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU A 639 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853
      removed outlier: 6.458A  pdb=" N   ALA A 849 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   VAL A 860 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)

    551 hydrogen bonds defined for protein.
    1617 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: 0.96

  Time building geometry restraints manager: 0.73 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: 2688
        1.34 -     1.46: 1995
        1.46 -     1.58: 4705
        1.58 -     1.69: 0
        1.69 -     1.81: 116
  Bond restraints: 9504
  Sorted by residual:
  bond pdb=" C   TYR A 393 "
       pdb=" N   PRO A 394 "
    ideal  model  delta    sigma   weight residual
    1.336  1.371 -0.035 1.20e-02 6.94e+03 8.31e+00
  bond pdb=" C   TYR B 393 "
       pdb=" N   PRO B 394 "
    ideal  model  delta    sigma   weight residual
    1.336  1.371 -0.035 1.20e-02 6.94e+03 8.31e+00
  bond pdb=" CA  PHE A 167 "
       pdb=" C   PHE A 167 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 1.23e-02 6.61e+03 4.16e+00
  bond pdb=" CA  PHE B 167 "
       pdb=" C   PHE B 167 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 1.23e-02 6.61e+03 4.02e+00
  bond pdb=" C   LEU A 557 "
       pdb=" O   LEU A 557 "
    ideal  model  delta    sigma   weight residual
    1.243  1.262 -0.019 9.50e-03 1.11e+04 3.89e+00
  ... (remaining 9499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 12526
        3.41 -     6.81: 318
        6.81 -    10.22: 56
       10.22 -    13.62: 12
       13.62 -    17.03: 2
  Bond angle restraints: 12914
  Sorted by residual:
  angle pdb=" C   PHE B 343 "
        pdb=" N   ASP B 344 "
        pdb=" CA  ASP B 344 "
      ideal   model   delta    sigma   weight residual
     121.70  134.09  -12.39 1.80e+00 3.09e-01 4.74e+01
  angle pdb=" C   PHE A 343 "
        pdb=" N   ASP A 344 "
        pdb=" CA  ASP A 344 "
      ideal   model   delta    sigma   weight residual
     121.70  134.00  -12.30 1.80e+00 3.09e-01 4.67e+01
  angle pdb=" C   PHE A 468 "
        pdb=" N   TRP A 469 "
        pdb=" CA  TRP A 469 "
      ideal   model   delta    sigma   weight residual
     122.56  111.11   11.45 1.72e+00 3.38e-01 4.43e+01
  angle pdb=" C   PHE B 468 "
        pdb=" N   TRP B 469 "
        pdb=" CA  TRP B 469 "
      ideal   model   delta    sigma   weight residual
     122.56  111.12   11.44 1.72e+00 3.38e-01 4.42e+01
  angle pdb=" C   LYS A 324 "
        pdb=" N   ASP A 325 "
        pdb=" CA  ASP A 325 "
      ideal   model   delta    sigma   weight residual
     121.56  129.31   -7.75 1.56e+00 4.11e-01 2.47e+01
  ... (remaining 12909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.04: 5000
       14.04 -    28.07: 384
       28.07 -    42.11: 140
       42.11 -    56.15: 18
       56.15 -    70.18: 14
  Dihedral angle restraints: 5556
    sinusoidal: 2114
      harmonic: 3442
  Sorted by residual:
  dihedral pdb=" CA  VAL B 327 "
           pdb=" C   VAL B 327 "
           pdb=" N   THR B 328 "
           pdb=" CA  THR B 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.15  -60.85     0      5.00e+00 4.00e-02 1.48e+02
  dihedral pdb=" CA  VAL A 327 "
           pdb=" C   VAL A 327 "
           pdb=" N   THR A 328 "
           pdb=" CA  THR A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.18  -60.82     0      5.00e+00 4.00e-02 1.48e+02
  dihedral pdb=" CA  GLY A 355 "
           pdb=" C   GLY A 355 "
           pdb=" N   ILE A 356 "
           pdb=" CA  ILE A 356 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.60  -42.40     0      5.00e+00 4.00e-02 7.19e+01
  ... (remaining 5553 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1105
       0.063 -    0.126: 342
       0.126 -    0.189: 63
       0.189 -    0.252: 12
       0.252 -    0.315: 4
  Chirality restraints: 1526
  Sorted by residual:
  chirality pdb=" CB  VAL A 489 "
            pdb=" CA  VAL A 489 "
            pdb=" CG1 VAL A 489 "
            pdb=" CG2 VAL A 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CB  VAL B 489 "
            pdb=" CA  VAL B 489 "
            pdb=" CG1 VAL B 489 "
            pdb=" CG2 VAL B 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CG  LEU A 843 "
            pdb=" CB  LEU A 843 "
            pdb=" CD1 LEU A 843 "
            pdb=" CD2 LEU A 843 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1523 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 352 "   -0.014 2.00e-02 2.50e+03   2.78e-02 7.70e+00
        pdb=" C   ALA B 352 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ALA B 352 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ALA B 353 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 352 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.66e+00
        pdb=" C   ALA A 352 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ALA A 352 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA A 353 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 406 "    0.045 5.00e-02 4.00e+02   6.88e-02 7.56e+00
        pdb=" N   PRO B 407 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 736
        2.73 -     3.27: 9839
        3.27 -     3.82: 16235
        3.82 -     4.36: 18375
        4.36 -     4.90: 29261
  Nonbonded interactions: 74446
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 401 "
            pdb=" OG1 THR A 405 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   ILE B 401 "
            pdb=" OG1 THR B 405 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   ILE B 472 "
            pdb=" OG1 THR B 476 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   ILE A 472 "
            pdb=" OG1 THR A 476 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OH  TYR B 302 "
            pdb=" O   GLU A 291 "
     model   vdw
     2.262 3.040
  ... (remaining 74441 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: 0.01
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:             1.440
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.190
  Find NCS groups from input model:        0.050
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
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      :  0.006   0.081   9504  Z= 0.312
  Angle     :  1.306  17.027  12914  Z= 0.709
  Chirality :  0.064   0.315   1526
  Planarity :  0.010   0.069   1580
  Dihedral  : 12.340  70.183   3340
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  9.34 %
    Favored  : 88.67 %
  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: -4.21 (0.20), residues: 1182
  helix: -2.24 (0.15), residues: 770
  sheet: -1.63 (1.13), residues: 20
  loop : -3.77 (0.25), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 669 
 TYR   0.042   0.004   TYR B 524 
 PHE   0.040   0.004   PHE B 468 
 TRP   0.029   0.003   TRP A 469 
 HIS   0.013   0.003   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 ( 9504)
  covalent geometry    : angle       1.30627 (12914)
  hydrogen bonds       : bond        0.15626 (  551)
  hydrogen bonds       : angle       7.13599 ( 1617)

*********************** 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
  222 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 202
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9467 (m-10) cc_final: 0.9225 (m-10)
REVERT: B  246 LEU cc_start: 0.9680 (tp) cc_final: 0.9375 (mt)
REVERT: B  449 TRP cc_start: 0.8575 (m100) cc_final: 0.8317 (m100)
REVERT: B  468 PHE cc_start: 0.9160 (p90) cc_final: 0.8852 (p90)
REVERT: B  471 SER cc_start: 0.9851 (OUTLIER) cc_final: 0.9239 (p)
REVERT: B  490 LEU cc_start: 0.9862 (OUTLIER) cc_final: 0.9430 (mm)
REVERT: B  494 PHE cc_start: 0.9472 (m-10) cc_final: 0.9193 (m-80)
REVERT: B  502 MET cc_start: 0.9668 (ptt) cc_final: 0.9412 (tmm)
REVERT: B  532 LEU cc_start: 0.9596 (tt) cc_final: 0.9237 (mp)
REVERT: A  178 PHE cc_start: 0.9448 (m-10) cc_final: 0.9204 (m-10)
REVERT: A  449 TRP cc_start: 0.8640 (m100) cc_final: 0.8386 (m100)
REVERT: A  468 PHE cc_start: 0.9098 (p90) cc_final: 0.8787 (p90)
REVERT: A  471 SER cc_start: 0.9849 (OUTLIER) cc_final: 0.9258 (p)
REVERT: A  490 LEU cc_start: 0.9862 (OUTLIER) cc_final: 0.9462 (mm)
REVERT: A  494 PHE cc_start: 0.9502 (m-10) cc_final: 0.9226 (m-80)
REVERT: A  502 MET cc_start: 0.9603 (ptt) cc_final: 0.9327 (tmm)
REVERT: A  532 LEU cc_start: 0.9579 (tt) cc_final: 0.9172 (mp)
REVERT: A  663 ARG cc_start: 0.8891 (mtm180) cc_final: 0.8587 (tpm170)
  outliers start: 20
  outliers final: 4
  residues processed: 209
  average time/residue: 0.0715
  time to fit residues: 22.4621
Evaluate side-chains
  136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.0370
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
B 451 HIS
B 662 GLN
B 823 GLN
B 838 HIS
A 379 HIS
A 451 HIS
A 838 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.051324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.041273 restraints weight = 70898.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.042516 restraints weight = 46923.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.043458 restraints weight = 34399.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.044046 restraints weight = 26992.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.044643 restraints weight = 22763.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9504  Z= 0.150
  Angle     :  0.790  10.136  12914  Z= 0.412
  Chirality :  0.045   0.160   1526
  Planarity :  0.007   0.055   1580
  Dihedral  :  6.887  50.707   1262
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  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: -2.56 (0.22), residues: 1182
  helix: -0.74 (0.18), residues: 766
  sheet: -1.10 (1.08), residues: 20
  loop : -3.63 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 669 
 TYR   0.021   0.002   TYR B 146 
 PHE   0.041   0.002   PHE B 461 
 TRP   0.029   0.002   TRP A 469 
 HIS   0.005   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9504)
  covalent geometry    : angle       0.79043 (12914)
  hydrogen bonds       : bond        0.04850 (  551)
  hydrogen bonds       : angle       4.85639 ( 1617)

*********************** 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
  172 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 LEU cc_start: 0.9629 (mt) cc_final: 0.9411 (mt)
REVERT: B  178 PHE cc_start: 0.9249 (m-10) cc_final: 0.9049 (m-80)
REVERT: B  246 LEU cc_start: 0.9716 (tp) cc_final: 0.9187 (tp)
REVERT: B  250 MET cc_start: 0.9321 (tpt) cc_final: 0.9041 (ppp)
REVERT: B  273 VAL cc_start: 0.9436 (t) cc_final: 0.9187 (m)
REVERT: B  339 MET cc_start: 0.9333 (pmm) cc_final: 0.9004 (pmm)
REVERT: B  466 MET cc_start: 0.9367 (tpt) cc_final: 0.9040 (mmm)
REVERT: B  468 PHE cc_start: 0.9173 (p90) cc_final: 0.8909 (p90)
REVERT: B  490 LEU cc_start: 0.9731 (pp) cc_final: 0.9453 (pp)
REVERT: B  494 PHE cc_start: 0.9365 (m-10) cc_final: 0.9091 (m-80)
REVERT: A  178 PHE cc_start: 0.9207 (m-10) cc_final: 0.8992 (m-80)
REVERT: A  246 LEU cc_start: 0.9761 (mt) cc_final: 0.9532 (mt)
REVERT: A  250 MET cc_start: 0.9346 (tpt) cc_final: 0.9079 (ppp)
REVERT: A  311 PHE cc_start: 0.9051 (m-80) cc_final: 0.8847 (m-80)
REVERT: A  339 MET cc_start: 0.9300 (pmm) cc_final: 0.8865 (pmm)
REVERT: A  468 PHE cc_start: 0.9128 (p90) cc_final: 0.8751 (p90)
REVERT: A  490 LEU cc_start: 0.9721 (pp) cc_final: 0.9468 (pp)
REVERT: A  494 PHE cc_start: 0.9361 (m-10) cc_final: 0.9114 (m-80)
REVERT: A  653 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9087 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0639
  time to fit residues: 16.8960
Evaluate side-chains
  128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 54 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 369 HIS
B 379 HIS
A 369 HIS
A 379 HIS
A 658 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.048060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.038351 restraints weight = 76530.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.039450 restraints weight = 51936.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.040293 restraints weight = 38800.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.040934 restraints weight = 30867.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.041429 restraints weight = 25732.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9504  Z= 0.176
  Angle     :  0.794  12.372  12914  Z= 0.407
  Chirality :  0.044   0.173   1526
  Planarity :  0.006   0.051   1580
  Dihedral  :  6.522  48.877   1262
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.37 %
    Favored  : 94.43 %
  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: -1.88 (0.23), residues: 1182
  helix: -0.21 (0.18), residues: 782
  sheet: -0.81 (1.07), residues: 20
  loop : -3.49 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 663 
 TYR   0.029   0.002   TYR B 146 
 PHE   0.036   0.002   PHE B 306 
 TRP   0.025   0.002   TRP B 469 
 HIS   0.004   0.001   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9504)
  covalent geometry    : angle       0.79391 (12914)
  hydrogen bonds       : bond        0.04656 (  551)
  hydrogen bonds       : angle       4.70334 ( 1617)

*********************** 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
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9220 (m-10) cc_final: 0.8978 (m-80)
REVERT: B  246 LEU cc_start: 0.9706 (tp) cc_final: 0.9282 (tp)
REVERT: B  250 MET cc_start: 0.9361 (tpt) cc_final: 0.9067 (ppp)
REVERT: B  339 MET cc_start: 0.9366 (pmm) cc_final: 0.8944 (pmm)
REVERT: B  466 MET cc_start: 0.9394 (tpt) cc_final: 0.9146 (tpp)
REVERT: B  470 MET cc_start: 0.9376 (ppp) cc_final: 0.9102 (ppp)
REVERT: B  490 LEU cc_start: 0.9735 (pp) cc_final: 0.9450 (pp)
REVERT: B  494 PHE cc_start: 0.9340 (m-10) cc_final: 0.9087 (m-80)
REVERT: B  663 ARG cc_start: 0.7602 (tpm170) cc_final: 0.7237 (tpm170)
REVERT: A  178 PHE cc_start: 0.9208 (m-10) cc_final: 0.8967 (m-80)
REVERT: A  250 MET cc_start: 0.9431 (tpt) cc_final: 0.9123 (ppp)
REVERT: A  311 PHE cc_start: 0.9046 (m-80) cc_final: 0.8784 (m-80)
REVERT: A  339 MET cc_start: 0.9311 (pmm) cc_final: 0.8826 (pmm)
REVERT: A  468 PHE cc_start: 0.9076 (p90) cc_final: 0.8783 (p90)
REVERT: A  490 LEU cc_start: 0.9825 (pp) cc_final: 0.9518 (pp)
REVERT: A  494 PHE cc_start: 0.9353 (m-10) cc_final: 0.9081 (m-80)
REVERT: A  532 LEU cc_start: 0.9479 (tp) cc_final: 0.9279 (tp)
REVERT: A  559 MET cc_start: 0.9656 (ptm) cc_final: 0.9320 (ptm)
REVERT: A  609 MET cc_start: 0.8586 (pmm) cc_final: 0.8340 (pmm)
REVERT: A  653 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9135 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0720
  time to fit residues: 18.1112
Evaluate side-chains
  114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 108 optimal weight:    0.8980
   chunk 79 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 823 GLN
** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.046285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.037172 restraints weight = 80758.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.038187 restraints weight = 54628.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.038966 restraints weight = 41077.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.039450 restraints weight = 32611.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.039952 restraints weight = 27811.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9504  Z= 0.244
  Angle     :  0.856  16.256  12914  Z= 0.440
  Chirality :  0.047   0.150   1526
  Planarity :  0.006   0.050   1580
  Dihedral  :  6.615  48.745   1262
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 23.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -1.64 (0.23), residues: 1182
  helix: -0.09 (0.18), residues: 782
  sheet:  None (None), residues: 0
  loop : -3.14 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 663 
 TYR   0.027   0.003   TYR B 146 
 PHE   0.052   0.003   PHE B 468 
 TRP   0.020   0.002   TRP B 469 
 HIS   0.005   0.002   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 9504)
  covalent geometry    : angle       0.85575 (12914)
  hydrogen bonds       : bond        0.04882 (  551)
  hydrogen bonds       : angle       4.83004 ( 1617)

*********************** 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
  144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 LEU cc_start: 0.9696 (mt) cc_final: 0.9405 (mt)
REVERT: B  232 GLU cc_start: 0.9604 (pm20) cc_final: 0.9216 (pt0)
REVERT: B  246 LEU cc_start: 0.9726 (tp) cc_final: 0.9249 (tp)
REVERT: B  250 MET cc_start: 0.9450 (tpt) cc_final: 0.9049 (ppp)
REVERT: B  339 MET cc_start: 0.9366 (pmm) cc_final: 0.9062 (pmm)
REVERT: B  466 MET cc_start: 0.9346 (tpt) cc_final: 0.9111 (tpp)
REVERT: B  470 MET cc_start: 0.9400 (ppp) cc_final: 0.9104 (ppp)
REVERT: B  494 PHE cc_start: 0.9292 (m-10) cc_final: 0.8940 (m-80)
REVERT: B  663 ARG cc_start: 0.7650 (tpm170) cc_final: 0.7348 (tpm170)
REVERT: A  232 GLU cc_start: 0.9625 (pm20) cc_final: 0.9244 (pt0)
REVERT: A  250 MET cc_start: 0.9445 (tpt) cc_final: 0.9121 (ppp)
REVERT: A  311 PHE cc_start: 0.8975 (m-80) cc_final: 0.8716 (m-80)
REVERT: A  339 MET cc_start: 0.9348 (pmm) cc_final: 0.9068 (pmm)
REVERT: A  461 PHE cc_start: 0.9377 (m-80) cc_final: 0.9165 (m-80)
REVERT: A  494 PHE cc_start: 0.9270 (m-10) cc_final: 0.8935 (m-80)
REVERT: A  532 LEU cc_start: 0.9559 (tp) cc_final: 0.9317 (tp)
REVERT: A  559 MET cc_start: 0.9675 (ptm) cc_final: 0.9343 (ptm)
REVERT: A  653 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9102 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0670
  time to fit residues: 14.8944
Evaluate side-chains
  111 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   chunk 67 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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 = 0.3178 r_free = 0.3178 target = 0.047805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.038320 restraints weight = 78257.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.039393 restraints weight = 52227.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.040235 restraints weight = 38145.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.040839 restraints weight = 30443.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.041259 restraints weight = 25491.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9504  Z= 0.155
  Angle     :  0.771  12.848  12914  Z= 0.391
  Chirality :  0.045   0.143   1526
  Planarity :  0.006   0.049   1580
  Dihedral  :  6.316  47.462   1262
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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: -1.26 (0.24), residues: 1182
  helix:  0.25 (0.18), residues: 782
  sheet: -1.15 (1.03), residues: 20
  loop : -3.15 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 663 
 TYR   0.021   0.002   TYR A 146 
 PHE   0.032   0.002   PHE A 463 
 TRP   0.021   0.001   TRP A 469 
 HIS   0.003   0.001   HIS B 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9504)
  covalent geometry    : angle       0.77085 (12914)
  hydrogen bonds       : bond        0.04515 (  551)
  hydrogen bonds       : angle       4.50240 ( 1617)

*********************** 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
  159 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9298 (m-10) cc_final: 0.9014 (m-80)
REVERT: B  246 LEU cc_start: 0.9726 (tp) cc_final: 0.9510 (mt)
REVERT: B  250 MET cc_start: 0.9437 (tpt) cc_final: 0.9082 (ppp)
REVERT: B  339 MET cc_start: 0.9325 (pmm) cc_final: 0.8903 (pmm)
REVERT: B  461 PHE cc_start: 0.9462 (m-80) cc_final: 0.9241 (m-80)
REVERT: B  468 PHE cc_start: 0.9124 (p90) cc_final: 0.8536 (p90)
REVERT: B  490 LEU cc_start: 0.9799 (pp) cc_final: 0.9522 (pp)
REVERT: B  494 PHE cc_start: 0.9202 (m-10) cc_final: 0.8907 (m-80)
REVERT: B  532 LEU cc_start: 0.9362 (tp) cc_final: 0.9096 (tp)
REVERT: B  663 ARG cc_start: 0.7475 (tpm170) cc_final: 0.7166 (tpm170)
REVERT: A  250 MET cc_start: 0.9448 (tpt) cc_final: 0.9127 (ppp)
REVERT: A  311 PHE cc_start: 0.9026 (m-80) cc_final: 0.8733 (m-80)
REVERT: A  339 MET cc_start: 0.9292 (pmm) cc_final: 0.8802 (pmm)
REVERT: A  461 PHE cc_start: 0.9455 (m-80) cc_final: 0.9205 (m-80)
REVERT: A  468 PHE cc_start: 0.9152 (p90) cc_final: 0.8740 (p90)
REVERT: A  490 LEU cc_start: 0.9748 (pp) cc_final: 0.9457 (pp)
REVERT: A  494 PHE cc_start: 0.9170 (m-10) cc_final: 0.8883 (m-80)
REVERT: A  532 LEU cc_start: 0.9488 (tp) cc_final: 0.9231 (tp)
REVERT: A  559 MET cc_start: 0.9650 (ptm) cc_final: 0.9295 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0679
  time to fit residues: 16.7169
Evaluate side-chains
  114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 96 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.9586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.048876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.038982 restraints weight = 75847.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.040103 restraints weight = 50965.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.040929 restraints weight = 37909.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.041546 restraints weight = 30317.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.041972 restraints weight = 25346.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.4623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9504  Z= 0.143
  Angle     :  0.771  10.680  12914  Z= 0.385
  Chirality :  0.045   0.169   1526
  Planarity :  0.005   0.048   1580
  Dihedral  :  6.044  46.925   1262
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  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: -1.09 (0.24), residues: 1182
  helix:  0.37 (0.18), residues: 786
  sheet: -0.89 (1.05), residues: 20
  loop : -3.11 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 663 
 TYR   0.015   0.001   TYR A 146 
 PHE   0.027   0.002   PHE A 547 
 TRP   0.036   0.002   TRP A 469 
 HIS   0.004   0.001   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9504)
  covalent geometry    : angle       0.77108 (12914)
  hydrogen bonds       : bond        0.04325 (  551)
  hydrogen bonds       : angle       4.37316 ( 1617)

*********************** 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
  167 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9269 (m-10) cc_final: 0.8980 (m-80)
REVERT: B  209 MET cc_start: 0.9513 (pmm) cc_final: 0.9114 (tmm)
REVERT: B  339 MET cc_start: 0.9313 (pmm) cc_final: 0.8921 (pmm)
REVERT: B  468 PHE cc_start: 0.9107 (p90) cc_final: 0.8693 (p90)
REVERT: B  490 LEU cc_start: 0.9784 (pp) cc_final: 0.9466 (pp)
REVERT: B  494 PHE cc_start: 0.9171 (m-10) cc_final: 0.8850 (m-80)
REVERT: B  532 LEU cc_start: 0.9264 (tp) cc_final: 0.8953 (tp)
REVERT: B  547 PHE cc_start: 0.9547 (p90) cc_final: 0.9303 (p90)
REVERT: B  663 ARG cc_start: 0.7375 (tpm170) cc_final: 0.7031 (tpm170)
REVERT: A  178 PHE cc_start: 0.9268 (m-10) cc_final: 0.8993 (m-80)
REVERT: A  250 MET cc_start: 0.9508 (tpt) cc_final: 0.9152 (ppp)
REVERT: A  311 PHE cc_start: 0.9082 (m-80) cc_final: 0.8671 (m-80)
REVERT: A  339 MET cc_start: 0.9281 (pmm) cc_final: 0.8825 (pmm)
REVERT: A  468 PHE cc_start: 0.9117 (p90) cc_final: 0.8854 (p90)
REVERT: A  490 LEU cc_start: 0.9775 (pp) cc_final: 0.9477 (pp)
REVERT: A  494 PHE cc_start: 0.9152 (m-10) cc_final: 0.8832 (m-80)
REVERT: A  527 ILE cc_start: 0.9309 (pt) cc_final: 0.9100 (pt)
REVERT: A  532 LEU cc_start: 0.9177 (tp) cc_final: 0.8865 (tp)
REVERT: A  559 MET cc_start: 0.9621 (ptm) cc_final: 0.9399 (ptm)
REVERT: A  663 ARG cc_start: 0.8005 (tpm170) cc_final: 0.7801 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0706
  time to fit residues: 18.2675
Evaluate side-chains
  124 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0050
   chunk 116 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0040
   chunk 39 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   overall best weight:    1.0008

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.050501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.040601 restraints weight = 73748.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.041778 restraints weight = 48956.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.042676 restraints weight = 35872.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.043313 restraints weight = 28227.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.043836 restraints weight = 23529.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4847

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= 0.145
  Angle     :  0.799  10.422  12914  Z= 0.399
  Chirality :  0.046   0.172   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.995  46.151   1262
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 18.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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: -0.91 (0.24), residues: 1182
  helix:  0.51 (0.19), residues: 776
  sheet: -0.68 (1.05), residues: 20
  loop : -2.96 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 654 
 TYR   0.023   0.002   TYR A 146 
 PHE   0.030   0.002   PHE B 306 
 TRP   0.021   0.001   TRP B 469 
 HIS   0.003   0.001   HIS B 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9504)
  covalent geometry    : angle       0.79869 (12914)
  hydrogen bonds       : bond        0.04384 (  551)
  hydrogen bonds       : angle       4.46181 ( 1617)

*********************** 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
  164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9296 (m-10) cc_final: 0.9023 (m-80)
REVERT: B  209 MET cc_start: 0.9527 (pmm) cc_final: 0.9143 (tmm)
REVERT: B  461 PHE cc_start: 0.9461 (m-80) cc_final: 0.9226 (m-80)
REVERT: B  490 LEU cc_start: 0.9794 (pp) cc_final: 0.9460 (pp)
REVERT: B  494 PHE cc_start: 0.9188 (m-10) cc_final: 0.8884 (m-80)
REVERT: B  532 LEU cc_start: 0.9280 (tp) cc_final: 0.8996 (tp)
REVERT: B  547 PHE cc_start: 0.9548 (p90) cc_final: 0.9133 (p90)
REVERT: B  559 MET cc_start: 0.9663 (ptm) cc_final: 0.9384 (ptm)
REVERT: B  663 ARG cc_start: 0.7395 (tpm170) cc_final: 0.7040 (tpm170)
REVERT: A  178 PHE cc_start: 0.9298 (m-10) cc_final: 0.9053 (m-80)
REVERT: A  250 MET cc_start: 0.9491 (tpt) cc_final: 0.9138 (ppp)
REVERT: A  311 PHE cc_start: 0.9105 (m-80) cc_final: 0.8678 (m-80)
REVERT: A  345 LEU cc_start: 0.9774 (pp) cc_final: 0.9540 (mt)
REVERT: A  461 PHE cc_start: 0.9450 (m-80) cc_final: 0.9229 (m-80)
REVERT: A  468 PHE cc_start: 0.9129 (p90) cc_final: 0.8843 (p90)
REVERT: A  490 LEU cc_start: 0.9793 (pp) cc_final: 0.9495 (pp)
REVERT: A  494 PHE cc_start: 0.9197 (m-10) cc_final: 0.8913 (m-80)
REVERT: A  532 LEU cc_start: 0.9247 (tp) cc_final: 0.8950 (tp)
REVERT: A  559 MET cc_start: 0.9607 (ptm) cc_final: 0.9341 (ptp)
REVERT: A  663 ARG cc_start: 0.7999 (tpm170) cc_final: 0.7778 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0693
  time to fit residues: 17.7122
Evaluate side-chains
  124 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.051142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.041202 restraints weight = 72537.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.042450 restraints weight = 47550.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.043368 restraints weight = 34584.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.044036 restraints weight = 26997.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.044532 restraints weight = 22258.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9504  Z= 0.146
  Angle     :  0.808  10.540  12914  Z= 0.402
  Chirality :  0.045   0.157   1526
  Planarity :  0.005   0.045   1580
  Dihedral  :  5.831  44.976   1262
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  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: -0.72 (0.24), residues: 1182
  helix:  0.67 (0.19), residues: 762
  sheet: -0.42 (1.01), residues: 20
  loop : -2.82 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 496 
 TYR   0.024   0.002   TYR A 146 
 PHE   0.030   0.002   PHE B 461 
 TRP   0.020   0.002   TRP A 469 
 HIS   0.003   0.001   HIS B 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9504)
  covalent geometry    : angle       0.80757 (12914)
  hydrogen bonds       : bond        0.04388 (  551)
  hydrogen bonds       : angle       4.40336 ( 1617)

*********************** 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
  168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9328 (m-10) cc_final: 0.9054 (m-80)
REVERT: B  209 MET cc_start: 0.9517 (pmm) cc_final: 0.9141 (tmm)
REVERT: B  461 PHE cc_start: 0.9494 (m-80) cc_final: 0.9252 (m-10)
REVERT: B  464 PHE cc_start: 0.9035 (p90) cc_final: 0.8718 (p90)
REVERT: B  468 PHE cc_start: 0.9065 (p90) cc_final: 0.8590 (p90)
REVERT: B  490 LEU cc_start: 0.9748 (pp) cc_final: 0.9395 (pp)
REVERT: B  494 PHE cc_start: 0.9180 (m-10) cc_final: 0.8783 (m-80)
REVERT: B  532 LEU cc_start: 0.9217 (tp) cc_final: 0.8891 (tp)
REVERT: B  547 PHE cc_start: 0.9547 (p90) cc_final: 0.9089 (p90)
REVERT: B  663 ARG cc_start: 0.7469 (tpm170) cc_final: 0.7099 (tpm170)
REVERT: A  178 PHE cc_start: 0.9319 (m-10) cc_final: 0.9066 (m-80)
REVERT: A  250 MET cc_start: 0.9456 (tpt) cc_final: 0.9148 (ppp)
REVERT: A  311 PHE cc_start: 0.9121 (m-80) cc_final: 0.8674 (m-80)
REVERT: A  461 PHE cc_start: 0.9486 (m-80) cc_final: 0.9258 (m-80)
REVERT: A  464 PHE cc_start: 0.9012 (p90) cc_final: 0.8698 (p90)
REVERT: A  468 PHE cc_start: 0.9071 (p90) cc_final: 0.8604 (p90)
REVERT: A  490 LEU cc_start: 0.9769 (pp) cc_final: 0.9430 (pp)
REVERT: A  494 PHE cc_start: 0.9156 (m-10) cc_final: 0.8761 (m-80)
REVERT: A  504 MET cc_start: 0.9578 (tmm) cc_final: 0.9337 (ppp)
REVERT: A  532 LEU cc_start: 0.9222 (tp) cc_final: 0.8875 (tp)
REVERT: A  547 PHE cc_start: 0.9527 (p90) cc_final: 0.9307 (p90)
REVERT: A  663 ARG cc_start: 0.7903 (tpm170) cc_final: 0.7669 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0658
  time to fit residues: 17.0697
Evaluate side-chains
  130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0040
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0870
   chunk 69 optimal weight:    5.9990
   overall best weight:    0.6172

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.052163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.042047 restraints weight = 74014.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.043285 restraints weight = 48872.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.044202 restraints weight = 35670.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.044899 restraints weight = 27927.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.045421 restraints weight = 22936.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5275

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= 0.141
  Angle     :  0.807  11.261  12914  Z= 0.401
  Chirality :  0.045   0.151   1526
  Planarity :  0.005   0.045   1580
  Dihedral  :  5.780  44.497   1262
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  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: -0.58 (0.25), residues: 1182
  helix:  0.86 (0.19), residues: 750
  sheet: -0.41 (0.97), residues: 20
  loop : -2.82 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 654 
 TYR   0.023   0.001   TYR A 146 
 PHE   0.033   0.002   PHE B 306 
 TRP   0.050   0.002   TRP B 469 
 HIS   0.003   0.001   HIS B 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9504)
  covalent geometry    : angle       0.80675 (12914)
  hydrogen bonds       : bond        0.04232 (  551)
  hydrogen bonds       : angle       4.31988 ( 1617)

*********************** 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
  177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9304 (m-10) cc_final: 0.9095 (m-80)
REVERT: B  209 MET cc_start: 0.9518 (pmm) cc_final: 0.9140 (tmm)
REVERT: B  464 PHE cc_start: 0.9089 (p90) cc_final: 0.8871 (p90)
REVERT: B  468 PHE cc_start: 0.9055 (p90) cc_final: 0.8770 (p90)
REVERT: B  490 LEU cc_start: 0.9738 (pp) cc_final: 0.9429 (pp)
REVERT: B  494 PHE cc_start: 0.9134 (m-10) cc_final: 0.8807 (m-80)
REVERT: B  532 LEU cc_start: 0.9253 (tp) cc_final: 0.8943 (tp)
REVERT: B  547 PHE cc_start: 0.9551 (p90) cc_final: 0.9167 (p90)
REVERT: B  663 ARG cc_start: 0.7447 (tpm170) cc_final: 0.7076 (tpm170)
REVERT: A  250 MET cc_start: 0.9453 (tpt) cc_final: 0.9138 (ppp)
REVERT: A  311 PHE cc_start: 0.9103 (m-80) cc_final: 0.8615 (m-80)
REVERT: A  464 PHE cc_start: 0.9043 (p90) cc_final: 0.8814 (p90)
REVERT: A  468 PHE cc_start: 0.9024 (p90) cc_final: 0.8712 (p90)
REVERT: A  490 LEU cc_start: 0.9738 (pp) cc_final: 0.9418 (pp)
REVERT: A  494 PHE cc_start: 0.9119 (m-10) cc_final: 0.8790 (m-80)
REVERT: A  504 MET cc_start: 0.9576 (tmm) cc_final: 0.9364 (ppp)
REVERT: A  532 LEU cc_start: 0.9226 (tp) cc_final: 0.8897 (tp)
REVERT: A  547 PHE cc_start: 0.9547 (p90) cc_final: 0.9238 (p90)
REVERT: A  559 MET cc_start: 0.9698 (ptm) cc_final: 0.9475 (ptm)
REVERT: A  663 ARG cc_start: 0.7873 (tpm170) cc_final: 0.7632 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0716
  time to fit residues: 19.4384
Evaluate side-chains
  130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3309 r_free = 0.3309 target = 0.050567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.040202 restraints weight = 74592.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.041465 restraints weight = 49554.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.042390 restraints weight = 36395.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.043080 restraints weight = 28613.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.043591 restraints weight = 23658.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9504  Z= 0.142
  Angle     :  0.812  10.997  12914  Z= 0.403
  Chirality :  0.045   0.155   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.716  44.610   1262
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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: -0.53 (0.24), residues: 1182
  helix:  0.89 (0.19), residues: 748
  sheet: -0.29 (0.96), residues: 20
  loop : -2.78 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 626 
 TYR   0.023   0.001   TYR A 146 
 PHE   0.036   0.002   PHE A 461 
 TRP   0.021   0.002   TRP B 469 
 HIS   0.004   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9504)
  covalent geometry    : angle       0.81167 (12914)
  hydrogen bonds       : bond        0.04224 (  551)
  hydrogen bonds       : angle       4.29525 ( 1617)

********************** 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
  179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9313 (m-10) cc_final: 0.9105 (m-80)
REVERT: B  209 MET cc_start: 0.9483 (pmm) cc_final: 0.9105 (tmm)
REVERT: B  279 PHE cc_start: 0.7375 (m-10) cc_final: 0.6934 (m-10)
REVERT: B  283 LEU cc_start: 0.9620 (pt) cc_final: 0.9322 (pt)
REVERT: B  354 ILE cc_start: 0.9530 (pt) cc_final: 0.9314 (pt)
REVERT: B  464 PHE cc_start: 0.9069 (p90) cc_final: 0.8845 (p90)
REVERT: B  468 PHE cc_start: 0.9079 (p90) cc_final: 0.8668 (p90)
REVERT: B  490 LEU cc_start: 0.9739 (pp) cc_final: 0.9431 (pp)
REVERT: B  494 PHE cc_start: 0.9147 (m-10) cc_final: 0.8821 (m-80)
REVERT: B  504 MET cc_start: 0.9555 (tmm) cc_final: 0.9323 (ppp)
REVERT: B  532 LEU cc_start: 0.9261 (tp) cc_final: 0.8948 (tp)
REVERT: B  547 PHE cc_start: 0.9527 (p90) cc_final: 0.9193 (p90)
REVERT: B  560 MET cc_start: 0.9837 (mpp) cc_final: 0.9426 (mpp)
REVERT: B  609 MET cc_start: 0.8652 (pmm) cc_final: 0.8450 (pmm)
REVERT: A  250 MET cc_start: 0.9449 (tpt) cc_final: 0.9128 (ppp)
REVERT: A  311 PHE cc_start: 0.9095 (m-80) cc_final: 0.8668 (m-80)
REVERT: A  354 ILE cc_start: 0.9560 (pt) cc_final: 0.9353 (pt)
REVERT: A  464 PHE cc_start: 0.9021 (p90) cc_final: 0.8787 (p90)
REVERT: A  468 PHE cc_start: 0.9058 (p90) cc_final: 0.8630 (p90)
REVERT: A  490 LEU cc_start: 0.9747 (pp) cc_final: 0.9414 (pp)
REVERT: A  494 PHE cc_start: 0.9124 (m-10) cc_final: 0.8793 (m-80)
REVERT: A  504 MET cc_start: 0.9572 (tmm) cc_final: 0.9372 (ppp)
REVERT: A  527 ILE cc_start: 0.9294 (pt) cc_final: 0.9090 (pt)
REVERT: A  532 LEU cc_start: 0.9265 (tp) cc_final: 0.8941 (tp)
REVERT: A  547 PHE cc_start: 0.9494 (p90) cc_final: 0.9149 (p90)
REVERT: A  559 MET cc_start: 0.9702 (ptm) cc_final: 0.9439 (ptm)
REVERT: A  663 ARG cc_start: 0.7833 (tpm170) cc_final: 0.7431 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0719
  time to fit residues: 19.7892
Evaluate side-chains
  127 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.050675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.040118 restraints weight = 71863.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.041386 restraints weight = 47820.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.042309 restraints weight = 35150.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.043002 restraints weight = 27674.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.043509 restraints weight = 22892.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.5603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9504  Z= 0.141
  Angle     :  0.805  10.677  12914  Z= 0.402
  Chirality :  0.045   0.165   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.659  45.965   1262
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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: -0.50 (0.25), residues: 1182
  helix:  0.81 (0.19), residues: 760
  sheet: -0.17 (0.97), residues: 20
  loop : -2.64 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 654 
 TYR   0.022   0.001   TYR A 146 
 PHE   0.037   0.002   PHE B 461 
 TRP   0.045   0.002   TRP B 469 
 HIS   0.003   0.001   HIS B 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9504)
  covalent geometry    : angle       0.80528 (12914)
  hydrogen bonds       : bond        0.04144 (  551)
  hydrogen bonds       : angle       4.31880 ( 1617)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1636.38 seconds
wall clock time: 28 minutes 58.22 seconds (1738.22 seconds total)