Starting phenix.real_space_refine
on Thu Feb 13 21:05:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvu_4657/02_2025/6qvu_4657.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvu_4657/02_2025/6qvu_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_4657/02_2025/6qvu_4657.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvu_4657/02_2025/6qvu_4657.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvu_4657/02_2025/6qvu_4657.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvu_4657/02_2025/6qvu_4657.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9272
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    B
  Time building chain proxies: 8.61, per 1000 atoms: 0.93
  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: 1.97
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.86
  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: 2.74

  Time building geometry restraints manager: 2.39 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.070
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.800
-------------------------------------------------------------------------------
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= 0.406
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (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
 TRP   0.029   0.003   TRP A 469 
 HIS   0.013   0.003   HIS B 451 
 PHE   0.040   0.004   PHE B 468 
 TYR   0.042   0.004   TYR B 524 
 ARG   0.016   0.001   ARG B 669 

*********************** 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  : 1.165 
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: 0.9238 (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: 0.8846 (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: 0.9215 (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: 0.9461 (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: 0.1903
  time to fit residues: 58.2000
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  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 47 optimal weight:    0.3980
   chunk 92 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 56 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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
B 451 HIS
B 662 GLN
B 838 HIS
A 369 HIS
A 379 HIS
A 451 HIS
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 838 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.049001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.039410 restraints weight = 73350.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.040563 restraints weight = 48820.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.041423 restraints weight = 36066.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9504  Z= 0.232
  Angle     :  0.822  13.293  12914  Z= 0.429
  Chirality :  0.045   0.174   1526
  Planarity :  0.007   0.068   1580
  Dihedral  :  7.198  51.508   1262
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.22), residues: 1182
  helix: -0.82 (0.18), residues: 776
  sheet: -1.34 (1.08), residues: 20
  loop : -3.69 (0.25), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 469 
 HIS   0.006   0.001   HIS B 451 
 PHE   0.048   0.003   PHE B 461 
 TYR   0.025   0.002   TYR B 146 
 ARG   0.011   0.001   ARG A 669 

*********************** 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
  153 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9335 (m-10) cc_final: 0.9056 (m-80)
REVERT: B  250 MET cc_start: 0.9378 (tpt) cc_final: 0.9079 (ppp)
REVERT: B  339 MET cc_start: 0.9343 (pmm) cc_final: 0.8997 (pmm)
REVERT: B  490 LEU cc_start: 0.9735 (pp) cc_final: 0.9464 (pp)
REVERT: B  494 PHE cc_start: 0.9397 (m-10) cc_final: 0.9120 (m-80)
REVERT: B  559 MET cc_start: 0.9691 (ptm) cc_final: 0.8863 (ptp)
REVERT: B  653 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9147 (mm-30)
REVERT: A  171 LEU cc_start: 0.9815 (mt) cc_final: 0.9582 (tp)
REVERT: A  178 PHE cc_start: 0.9277 (m-10) cc_final: 0.9009 (m-80)
REVERT: A  250 MET cc_start: 0.9417 (tpt) cc_final: 0.9096 (ppp)
REVERT: A  339 MET cc_start: 0.9343 (pmm) cc_final: 0.8904 (pmm)
REVERT: A  490 LEU cc_start: 0.9720 (pp) cc_final: 0.9483 (pp)
REVERT: A  494 PHE cc_start: 0.9391 (m-10) cc_final: 0.9157 (m-80)
REVERT: A  653 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9137 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1801
  time to fit residues: 40.6136
Evaluate side-chains
  115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.047412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.037947 restraints weight = 77397.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.039038 restraints weight = 52117.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.039864 restraints weight = 38605.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9504  Z= 0.237
  Angle     :  0.796  13.635  12914  Z= 0.410
  Chirality :  0.044   0.174   1526
  Planarity :  0.006   0.050   1580
  Dihedral  :  6.759  49.715   1262
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.57 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.23), residues: 1182
  helix: -0.23 (0.18), residues: 782
  sheet: -1.28 (1.01), residues: 20
  loop : -3.65 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 469 
 HIS   0.004   0.001   HIS B 835 
 PHE   0.036   0.002   PHE B 306 
 TYR   0.028   0.002   TYR B 146 
 ARG   0.004   0.001   ARG B 300 

*********************** 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
  158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.859 
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: 0.9274 (m-10) cc_final: 0.9021 (m-80)
REVERT: B  232 GLU cc_start: 0.9558 (OUTLIER) cc_final: 0.9277 (pt0)
REVERT: B  246 LEU cc_start: 0.9803 (mm) cc_final: 0.9538 (mt)
REVERT: B  250 MET cc_start: 0.9406 (tpt) cc_final: 0.9103 (ppp)
REVERT: B  339 MET cc_start: 0.9330 (pmm) cc_final: 0.8913 (pmm)
REVERT: B  468 PHE cc_start: 0.9123 (p90) cc_final: 0.8713 (p90)
REVERT: B  490 LEU cc_start: 0.9716 (pp) cc_final: 0.9387 (pp)
REVERT: B  494 PHE cc_start: 0.9336 (m-10) cc_final: 0.9041 (m-80)
REVERT: B  653 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9167 (mm-30)
REVERT: A  124 LEU cc_start: 0.9764 (tt) cc_final: 0.9446 (tt)
REVERT: A  128 MET cc_start: 0.9569 (mmp) cc_final: 0.9300 (mmm)
REVERT: A  171 LEU cc_start: 0.9810 (mt) cc_final: 0.9533 (tp)
REVERT: A  178 PHE cc_start: 0.9257 (m-10) cc_final: 0.8958 (m-10)
REVERT: A  232 GLU cc_start: 0.9579 (OUTLIER) cc_final: 0.9280 (pt0)
REVERT: A  246 LEU cc_start: 0.9740 (mt) cc_final: 0.9532 (mt)
REVERT: A  250 MET cc_start: 0.9438 (tpt) cc_final: 0.9128 (ppp)
REVERT: A  311 PHE cc_start: 0.9050 (m-80) cc_final: 0.8823 (m-80)
REVERT: A  339 MET cc_start: 0.9315 (pmm) cc_final: 0.8872 (pmm)
REVERT: A  468 PHE cc_start: 0.9113 (p90) cc_final: 0.8806 (p90)
REVERT: A  494 PHE cc_start: 0.9362 (m-10) cc_final: 0.9027 (m-80)
REVERT: A  532 LEU cc_start: 0.9519 (tp) cc_final: 0.9317 (tp)
REVERT: A  559 MET cc_start: 0.9673 (ptm) cc_final: 0.9354 (ptm)
REVERT: A  609 MET cc_start: 0.8652 (pmm) cc_final: 0.8441 (pmm)
REVERT: A  653 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9141 (mm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1711
  time to fit residues: 39.5634
Evaluate side-chains
  123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0060
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    1.1200

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.048580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.038668 restraints weight = 73291.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.039791 restraints weight = 50139.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.040630 restraints weight = 37567.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9504  Z= 0.199
  Angle     :  0.762  10.835  12914  Z= 0.386
  Chirality :  0.044   0.148   1526
  Planarity :  0.006   0.051   1580
  Dihedral  :  6.331  48.453   1262
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.24), residues: 1182
  helix:  0.13 (0.19), residues: 782
  sheet: -1.13 (1.00), residues: 20
  loop : -3.37 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 469 
 HIS   0.005   0.001   HIS B 664 
 PHE   0.026   0.002   PHE B 547 
 TYR   0.025   0.002   TYR B 146 
 ARG   0.002   0.000   ARG A 654 

*********************** 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
  166 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.118 
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: B  178 PHE cc_start: 0.9226 (m-10) cc_final: 0.8984 (m-80)
REVERT: B  246 LEU cc_start: 0.9798 (mm) cc_final: 0.9537 (mt)
REVERT: B  250 MET cc_start: 0.9386 (tpt) cc_final: 0.9092 (ppp)
REVERT: B  339 MET cc_start: 0.9363 (pmm) cc_final: 0.9082 (pmm)
REVERT: B  490 LEU cc_start: 0.9728 (pp) cc_final: 0.9405 (pp)
REVERT: B  494 PHE cc_start: 0.9287 (m-10) cc_final: 0.8927 (m-80)
REVERT: B  559 MET cc_start: 0.9682 (ptm) cc_final: 0.8898 (ppp)
REVERT: B  560 MET cc_start: 0.9827 (mpp) cc_final: 0.9278 (mpp)
REVERT: B  609 MET cc_start: 0.8647 (pmm) cc_final: 0.8388 (pmm)
REVERT: B  663 ARG cc_start: 0.7648 (tpm170) cc_final: 0.7311 (tpm170)
REVERT: A  178 PHE cc_start: 0.9231 (m-10) cc_final: 0.9001 (m-80)
REVERT: A  250 MET cc_start: 0.9439 (tpt) cc_final: 0.9109 (ppp)
REVERT: A  311 PHE cc_start: 0.9042 (m-80) cc_final: 0.8768 (m-80)
REVERT: A  339 MET cc_start: 0.9340 (pmm) cc_final: 0.9065 (pmm)
REVERT: A  468 PHE cc_start: 0.9094 (p90) cc_final: 0.8848 (p90)
REVERT: A  490 LEU cc_start: 0.9762 (pp) cc_final: 0.9477 (pp)
REVERT: A  494 PHE cc_start: 0.9273 (m-10) cc_final: 0.8971 (m-80)
REVERT: A  532 LEU cc_start: 0.9395 (tp) cc_final: 0.9149 (tp)
REVERT: A  559 MET cc_start: 0.9642 (ptm) cc_final: 0.9352 (ptm)
REVERT: A  609 MET cc_start: 0.8637 (pmm) cc_final: 0.8421 (pmm)
REVERT: A  653 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9133 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1740
  time to fit residues: 42.8295
Evaluate side-chains
  120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 47 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 103 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 436 HIS
B 658 GLN
** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.048573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.038747 restraints weight = 74941.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.039872 restraints weight = 50864.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.040735 restraints weight = 37964.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9504  Z= 0.200
  Angle     :  0.766  12.936  12914  Z= 0.388
  Chirality :  0.045   0.175   1526
  Planarity :  0.006   0.049   1580
  Dihedral  :  6.149  46.900   1262
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.24), residues: 1182
  helix:  0.22 (0.18), residues: 782
  sheet: -0.91 (1.00), residues: 20
  loop : -3.21 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 469 
 HIS   0.004   0.001   HIS B 389 
 PHE   0.049   0.003   PHE B 461 
 TYR   0.024   0.002   TYR B 146 
 ARG   0.003   0.000   ARG A 654 

*********************** 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
  156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9255 (m-10) cc_final: 0.8943 (m-80)
REVERT: B  209 MET cc_start: 0.9498 (pmm) cc_final: 0.9114 (tmm)
REVERT: B  250 MET cc_start: 0.9437 (tpt) cc_final: 0.9090 (ppp)
REVERT: B  339 MET cc_start: 0.9340 (pmm) cc_final: 0.8958 (pmm)
REVERT: B  468 PHE cc_start: 0.9077 (p90) cc_final: 0.8783 (p90)
REVERT: B  490 LEU cc_start: 0.9796 (pp) cc_final: 0.9423 (pp)
REVERT: B  494 PHE cc_start: 0.9290 (m-10) cc_final: 0.8949 (m-80)
REVERT: B  532 LEU cc_start: 0.9315 (tp) cc_final: 0.8835 (tp)
REVERT: B  609 MET cc_start: 0.8605 (pmm) cc_final: 0.8362 (pmm)
REVERT: B  663 ARG cc_start: 0.7740 (tpm170) cc_final: 0.7367 (tpm170)
REVERT: A  124 LEU cc_start: 0.9662 (tt) cc_final: 0.9249 (tt)
REVERT: A  250 MET cc_start: 0.9457 (tpt) cc_final: 0.9150 (ppp)
REVERT: A  311 PHE cc_start: 0.9077 (m-80) cc_final: 0.8726 (m-80)
REVERT: A  339 MET cc_start: 0.9327 (pmm) cc_final: 0.8844 (pmm)
REVERT: A  461 PHE cc_start: 0.9440 (m-80) cc_final: 0.9205 (m-80)
REVERT: A  468 PHE cc_start: 0.9090 (p90) cc_final: 0.8680 (p90)
REVERT: A  490 LEU cc_start: 0.9782 (pp) cc_final: 0.9462 (pp)
REVERT: A  494 PHE cc_start: 0.9262 (m-10) cc_final: 0.8939 (m-80)
REVERT: A  532 LEU cc_start: 0.9434 (tp) cc_final: 0.9151 (tp)
REVERT: A  559 MET cc_start: 0.9636 (ptm) cc_final: 0.9307 (ptm)
REVERT: A  609 MET cc_start: 0.8572 (pmm) cc_final: 0.8365 (pmm)
REVERT: A  653 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9138 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1647
  time to fit residues: 38.8528
Evaluate side-chains
  112 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0010
   chunk 52 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 102 optimal weight:    0.5980
   chunk 113 optimal weight:    9.9990
   overall best weight:    1.2590

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.048975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.039119 restraints weight = 73423.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.040288 restraints weight = 49732.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.041162 restraints weight = 36967.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4404

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= 0.207
  Angle     :  0.785  13.150  12914  Z= 0.390
  Chirality :  0.046   0.274   1526
  Planarity :  0.005   0.048   1580
  Dihedral  :  6.053  45.551   1262
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.24), residues: 1182
  helix:  0.49 (0.19), residues: 768
  sheet: -0.83 (0.99), residues: 20
  loop : -3.09 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 433 
 HIS   0.003   0.001   HIS A 538 
 PHE   0.040   0.002   PHE B 461 
 TYR   0.021   0.001   TYR B 146 
 ARG   0.003   0.000   ARG A 496 

*********************** 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
  158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9249 (m-10) cc_final: 0.8974 (m-80)
REVERT: B  209 MET cc_start: 0.9488 (pmm) cc_final: 0.9116 (tmm)
REVERT: B  246 LEU cc_start: 0.9779 (mm) cc_final: 0.9525 (mt)
REVERT: B  250 MET cc_start: 0.9440 (tpt) cc_final: 0.9076 (ppp)
REVERT: B  325 ASP cc_start: 0.8219 (m-30) cc_final: 0.7984 (p0)
REVERT: B  339 MET cc_start: 0.9350 (pmm) cc_final: 0.8986 (pmm)
REVERT: B  468 PHE cc_start: 0.9145 (p90) cc_final: 0.8600 (p90)
REVERT: B  490 LEU cc_start: 0.9797 (pp) cc_final: 0.9496 (pp)
REVERT: B  494 PHE cc_start: 0.9280 (m-10) cc_final: 0.8994 (m-80)
REVERT: B  532 LEU cc_start: 0.9317 (tp) cc_final: 0.9021 (tp)
REVERT: B  609 MET cc_start: 0.8634 (pmm) cc_final: 0.8396 (pmm)
REVERT: B  663 ARG cc_start: 0.7811 (tpm170) cc_final: 0.7493 (tpm170)
REVERT: A  178 PHE cc_start: 0.9236 (m-10) cc_final: 0.8932 (m-80)
REVERT: A  250 MET cc_start: 0.9450 (tpt) cc_final: 0.9131 (ppp)
REVERT: A  311 PHE cc_start: 0.9097 (m-80) cc_final: 0.8708 (m-80)
REVERT: A  339 MET cc_start: 0.9311 (pmm) cc_final: 0.8874 (pmm)
REVERT: A  461 PHE cc_start: 0.9457 (m-80) cc_final: 0.9201 (m-10)
REVERT: A  468 PHE cc_start: 0.9093 (p90) cc_final: 0.8657 (p90)
REVERT: A  485 MET cc_start: 0.9587 (mtm) cc_final: 0.9312 (mtm)
REVERT: A  490 LEU cc_start: 0.9812 (pp) cc_final: 0.9480 (pp)
REVERT: A  494 PHE cc_start: 0.9270 (m-10) cc_final: 0.8961 (m-80)
REVERT: A  527 ILE cc_start: 0.9317 (pt) cc_final: 0.9085 (pt)
REVERT: A  532 LEU cc_start: 0.9182 (tp) cc_final: 0.8736 (tp)
REVERT: A  609 MET cc_start: 0.8552 (pmm) cc_final: 0.8345 (pmm)
REVERT: A  653 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9131 (mm-30)
REVERT: A  663 ARG cc_start: 0.7781 (tpm170) cc_final: 0.7481 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1735
  time to fit residues: 41.2602
Evaluate side-chains
  116 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 101 optimal weight:    8.9990
   chunk 54 optimal weight:    0.5980
   chunk 90 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.048668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.038979 restraints weight = 76223.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.040127 restraints weight = 51577.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.040967 restraints weight = 38382.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4608

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= 0.219
  Angle     :  0.788  12.888  12914  Z= 0.393
  Chirality :  0.045   0.172   1526
  Planarity :  0.005   0.045   1580
  Dihedral  :  5.992  44.855   1262
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.24), residues: 1182
  helix:  0.54 (0.19), residues: 772
  sheet: -0.86 (0.97), residues: 20
  loop : -2.98 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 469 
 HIS   0.003   0.001   HIS B 835 
 PHE   0.033   0.002   PHE B 306 
 TYR   0.022   0.002   TYR A 146 
 ARG   0.003   0.000   ARG A 654 

*********************** 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
  159 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9300 (m-10) cc_final: 0.9043 (m-80)
REVERT: B  209 MET cc_start: 0.9501 (pmm) cc_final: 0.9126 (tmm)
REVERT: B  246 LEU cc_start: 0.9781 (mm) cc_final: 0.9526 (mt)
REVERT: B  250 MET cc_start: 0.9491 (tpt) cc_final: 0.9129 (ppp)
REVERT: B  325 ASP cc_start: 0.8015 (m-30) cc_final: 0.7811 (p0)
REVERT: B  461 PHE cc_start: 0.9487 (m-80) cc_final: 0.9228 (m-10)
REVERT: B  468 PHE cc_start: 0.9108 (p90) cc_final: 0.8756 (p90)
REVERT: B  490 LEU cc_start: 0.9786 (pp) cc_final: 0.9509 (pp)
REVERT: B  494 PHE cc_start: 0.9210 (m-10) cc_final: 0.8922 (m-80)
REVERT: B  532 LEU cc_start: 0.9394 (tp) cc_final: 0.9140 (tp)
REVERT: B  609 MET cc_start: 0.8724 (pmm) cc_final: 0.8511 (pmm)
REVERT: B  663 ARG cc_start: 0.7655 (tpm170) cc_final: 0.7333 (tpm170)
REVERT: A  178 PHE cc_start: 0.9286 (m-10) cc_final: 0.9068 (m-80)
REVERT: A  250 MET cc_start: 0.9480 (tpt) cc_final: 0.9134 (ppp)
REVERT: A  311 PHE cc_start: 0.9078 (m-80) cc_final: 0.8701 (m-80)
REVERT: A  325 ASP cc_start: 0.8022 (m-30) cc_final: 0.7696 (p0)
REVERT: A  461 PHE cc_start: 0.9500 (m-80) cc_final: 0.9298 (m-80)
REVERT: A  468 PHE cc_start: 0.9150 (p90) cc_final: 0.8791 (p90)
REVERT: A  490 LEU cc_start: 0.9793 (pp) cc_final: 0.9472 (pp)
REVERT: A  494 PHE cc_start: 0.9248 (m-10) cc_final: 0.8912 (m-80)
REVERT: A  532 LEU cc_start: 0.9317 (tp) cc_final: 0.8940 (tp)
REVERT: A  653 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9109 (mm-30)
REVERT: A  663 ARG cc_start: 0.7690 (tpm170) cc_final: 0.7429 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1789
  time to fit residues: 42.0948
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  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0030
   chunk 44 optimal weight:    0.5980
   chunk 86 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.051248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.041233 restraints weight = 72313.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.042479 restraints weight = 47839.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.043400 restraints weight = 34963.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4928

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= 0.194
  Angle     :  0.791  10.833  12914  Z= 0.390
  Chirality :  0.046   0.160   1526
  Planarity :  0.005   0.046   1580
  Dihedral  :  5.805  44.311   1262
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1182
  helix:  0.81 (0.19), residues: 746
  sheet: -0.81 (0.95), residues: 20
  loop : -2.92 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 469 
 HIS   0.009   0.001   HIS A 847 
 PHE   0.034   0.002   PHE B 306 
 TYR   0.018   0.001   TYR A 146 
 ARG   0.002   0.000   ARG A 654 

*********************** 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
  170 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.9493 (pmm) cc_final: 0.9149 (tmm)
REVERT: B  246 LEU cc_start: 0.9774 (mm) cc_final: 0.9517 (mt)
REVERT: B  250 MET cc_start: 0.9485 (tpt) cc_final: 0.9139 (ppp)
REVERT: B  461 PHE cc_start: 0.9480 (m-80) cc_final: 0.9271 (m-80)
REVERT: B  490 LEU cc_start: 0.9773 (pp) cc_final: 0.9471 (pp)
REVERT: B  494 PHE cc_start: 0.9237 (m-10) cc_final: 0.8853 (m-80)
REVERT: B  532 LEU cc_start: 0.9251 (tp) cc_final: 0.8919 (tp)
REVERT: B  547 PHE cc_start: 0.9534 (p90) cc_final: 0.9139 (p90)
REVERT: B  559 MET cc_start: 0.9673 (ptm) cc_final: 0.9435 (ptm)
REVERT: B  609 MET cc_start: 0.8473 (pmm) cc_final: 0.8249 (pmm)
REVERT: B  663 ARG cc_start: 0.7412 (tpm170) cc_final: 0.7059 (tpm170)
REVERT: A  250 MET cc_start: 0.9475 (tpt) cc_final: 0.9144 (ppp)
REVERT: A  311 PHE cc_start: 0.9117 (m-80) cc_final: 0.8730 (m-80)
REVERT: A  461 PHE cc_start: 0.9449 (m-80) cc_final: 0.9239 (m-80)
REVERT: A  468 PHE cc_start: 0.9082 (p90) cc_final: 0.8822 (p90)
REVERT: A  490 LEU cc_start: 0.9777 (pp) cc_final: 0.9470 (pp)
REVERT: A  494 PHE cc_start: 0.9194 (m-10) cc_final: 0.8820 (m-80)
REVERT: A  532 LEU cc_start: 0.9188 (tp) cc_final: 0.8662 (tp)
REVERT: A  547 PHE cc_start: 0.9556 (p90) cc_final: 0.9325 (p90)
REVERT: A  663 ARG cc_start: 0.7645 (tpm170) cc_final: 0.7365 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1697
  time to fit residues: 42.7380
Evaluate side-chains
  126 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 58 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.050296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.039214 restraints weight = 76935.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.040562 restraints weight = 48602.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.041566 restraints weight = 34647.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5135

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= 0.220
  Angle     :  0.824  11.811  12914  Z= 0.415
  Chirality :  0.046   0.157   1526
  Planarity :  0.005   0.046   1580
  Dihedral  :  5.873  44.038   1262
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1182
  helix:  0.63 (0.19), residues: 762
  sheet: -0.60 (0.98), residues: 20
  loop : -2.76 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 469 
 HIS   0.006   0.001   HIS B 847 
 PHE   0.029   0.002   PHE A 306 
 TYR   0.017   0.002   TYR A 146 
 ARG   0.003   0.000   ARG A 654 

*********************** 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
  156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.9488 (pmm) cc_final: 0.9126 (tmm)
REVERT: B  250 MET cc_start: 0.9478 (tpt) cc_final: 0.9137 (ppp)
REVERT: B  461 PHE cc_start: 0.9454 (m-80) cc_final: 0.9242 (m-80)
REVERT: B  468 PHE cc_start: 0.9108 (p90) cc_final: 0.8792 (p90)
REVERT: B  490 LEU cc_start: 0.9754 (pp) cc_final: 0.9441 (pp)
REVERT: B  494 PHE cc_start: 0.9204 (m-10) cc_final: 0.8911 (m-80)
REVERT: B  532 LEU cc_start: 0.9427 (tp) cc_final: 0.9165 (tp)
REVERT: B  663 ARG cc_start: 0.7459 (tpm170) cc_final: 0.7108 (tpm170)
REVERT: A  250 MET cc_start: 0.9451 (tpt) cc_final: 0.9119 (ppp)
REVERT: A  311 PHE cc_start: 0.9108 (m-80) cc_final: 0.8703 (m-80)
REVERT: A  490 LEU cc_start: 0.9783 (pp) cc_final: 0.9546 (pp)
REVERT: A  494 PHE cc_start: 0.9205 (m-10) cc_final: 0.8936 (m-80)
REVERT: A  532 LEU cc_start: 0.9314 (tp) cc_final: 0.8945 (tp)
REVERT: A  559 MET cc_start: 0.9731 (ptm) cc_final: 0.9480 (ptm)
REVERT: A  663 ARG cc_start: 0.7684 (tpm170) cc_final: 0.7413 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1743
  time to fit residues: 40.4463
Evaluate side-chains
  117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 70 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 81 optimal weight:    0.4980
   chunk 109 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0980
   chunk 84 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.050617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.039965 restraints weight = 74247.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.041215 restraints weight = 49783.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.042134 restraints weight = 36837.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5376

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= 0.200
  Angle     :  0.827  11.041  12914  Z= 0.415
  Chirality :  0.047   0.233   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.710  44.200   1262
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1182
  helix:  0.86 (0.19), residues: 746
  sheet: -0.46 (1.01), residues: 20
  loop : -2.72 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 469 
 HIS   0.006   0.001   HIS A 847 
 PHE   0.037   0.002   PHE B 306 
 TYR   0.014   0.001   TYR B 146 
 ARG   0.002   0.000   ARG A 654 

********************** 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
  170 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.909 
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: B  178 PHE cc_start: 0.9510 (m-80) cc_final: 0.9190 (m-80)
REVERT: B  209 MET cc_start: 0.9450 (pmm) cc_final: 0.9108 (tmm)
REVERT: B  246 LEU cc_start: 0.9815 (mm) cc_final: 0.9573 (mt)
REVERT: B  250 MET cc_start: 0.9478 (tpt) cc_final: 0.9139 (ppp)
REVERT: B  279 PHE cc_start: 0.7523 (m-10) cc_final: 0.7076 (m-10)
REVERT: B  461 PHE cc_start: 0.9367 (m-80) cc_final: 0.9103 (m-80)
REVERT: B  468 PHE cc_start: 0.9125 (p90) cc_final: 0.8820 (p90)
REVERT: B  490 LEU cc_start: 0.9752 (pp) cc_final: 0.9292 (mt)
REVERT: B  494 PHE cc_start: 0.9176 (m-10) cc_final: 0.8940 (m-80)
REVERT: B  532 LEU cc_start: 0.9304 (tp) cc_final: 0.9070 (tp)
REVERT: B  547 PHE cc_start: 0.9496 (p90) cc_final: 0.9288 (p90)
REVERT: B  560 MET cc_start: 0.9858 (mpp) cc_final: 0.9476 (mpp)
REVERT: B  609 MET cc_start: 0.8483 (pmm) cc_final: 0.8249 (pmm)
REVERT: A  250 MET cc_start: 0.9477 (tpt) cc_final: 0.9147 (ppp)
REVERT: A  311 PHE cc_start: 0.9116 (m-80) cc_final: 0.8656 (m-80)
REVERT: A  461 PHE cc_start: 0.9446 (m-80) cc_final: 0.9207 (m-80)
REVERT: A  468 PHE cc_start: 0.8986 (p90) cc_final: 0.8738 (p90)
REVERT: A  490 LEU cc_start: 0.9767 (pp) cc_final: 0.9520 (pp)
REVERT: A  494 PHE cc_start: 0.9184 (m-10) cc_final: 0.8877 (m-80)
REVERT: A  504 MET cc_start: 0.9636 (tmm) cc_final: 0.9378 (ppp)
REVERT: A  532 LEU cc_start: 0.9236 (tp) cc_final: 0.8962 (tp)
REVERT: A  559 MET cc_start: 0.9699 (ptm) cc_final: 0.9444 (ptm)
REVERT: A  609 MET cc_start: 0.8644 (pmm) cc_final: 0.8441 (pmm)
REVERT: A  663 ARG cc_start: 0.7666 (tpm170) cc_final: 0.7108 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1736
  time to fit residues: 43.6671
Evaluate side-chains
  136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0040
   chunk 17 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 114 optimal weight:    8.9990
   overall best weight:    1.3198

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

Flipped N/Q/H residues before XYZ refinement:
** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.051371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.039903 restraints weight = 75378.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.041249 restraints weight = 48267.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.042298 restraints weight = 34558.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.5516

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= 0.206
  Angle     :  0.812  10.716  12914  Z= 0.407
  Chirality :  0.046   0.158   1526
  Planarity :  0.005   0.046   1580
  Dihedral  :  5.670  43.514   1262
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.25), residues: 1182
  helix:  0.79 (0.19), residues: 758
  sheet: -0.32 (1.00), residues: 20
  loop : -2.71 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 469 
 HIS   0.005   0.001   HIS A 847 
 PHE   0.035   0.002   PHE B 306 
 TYR   0.015   0.001   TYR B 146 
 ARG   0.002   0.000   ARG B 654 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2875.07 seconds
wall clock time: 52 minutes 28.26 seconds (3148.26 seconds total)