Starting phenix.real_space_refine
on Wed Apr 30 09:10:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvu_4657/04_2025/6qvu_4657.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvu_4657/04_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_4657/04_2025/6qvu_4657.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvu_4657/04_2025/6qvu_4657.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvu_4657/04_2025/6qvu_4657.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvu_4657/04_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-5669/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: 8.56, per 1000 atoms: 0.92
  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.91
  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: 2.42

  Time building geometry restraints manager: 2.69 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: 0.04
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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     26.350
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.710
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 1.025 
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: 0.1702
  time to fit residues: 52.2712
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  : 0.959 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.039410 restraints weight = 73350.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.040565 restraints weight = 48822.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.041433 restraints weight = 36052.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
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= 0.180
  Angle     :  0.822  13.293  12914  Z= 0.429
  Chirality :  0.045   0.174   1526
  Planarity :  0.007   0.068   1580
  Dihedral  :  7.198  51.509   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05039 (  551)
  hydrogen bonds       : angle       5.02875 ( 1617)
  covalent geometry    : bond        0.00358 ( 9504)
  covalent geometry    : angle       0.82190 (12914)

*********************** 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  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9336 (m-10) cc_final: 0.9057 (m-80)
REVERT: B  250 MET cc_start: 0.9379 (tpt) cc_final: 0.9080 (ppp)
REVERT: B  339 MET cc_start: 0.9344 (pmm) cc_final: 0.8998 (pmm)
REVERT: B  490 LEU cc_start: 0.9735 (pp) cc_final: 0.9463 (pp)
REVERT: B  494 PHE cc_start: 0.9396 (m-10) cc_final: 0.9119 (m-80)
REVERT: B  559 MET cc_start: 0.9691 (ptm) cc_final: 0.8863 (ptp)
REVERT: B  653 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9147 (mm-30)
REVERT: A  171 LEU cc_start: 0.9815 (mt) cc_final: 0.9581 (tp)
REVERT: A  178 PHE cc_start: 0.9277 (m-10) cc_final: 0.9008 (m-80)
REVERT: A  250 MET cc_start: 0.9417 (tpt) cc_final: 0.9097 (ppp)
REVERT: A  339 MET cc_start: 0.9344 (pmm) cc_final: 0.8904 (pmm)
REVERT: A  490 LEU cc_start: 0.9720 (pp) cc_final: 0.9481 (pp)
REVERT: A  494 PHE cc_start: 0.9392 (m-10) cc_final: 0.9157 (m-80)
REVERT: A  653 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9137 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1647
  time to fit residues: 37.6632
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  : 0.950 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 64 optimal weight:    0.3980
   chunk 111 optimal weight:    0.8980
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3202 r_free = 0.3202 target = 0.048367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.038610 restraints weight = 75977.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.039755 restraints weight = 51359.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.040614 restraints weight = 38155.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9504  Z= 0.153
  Angle     :  0.778  11.525  12914  Z= 0.398
  Chirality :  0.044   0.179   1526
  Planarity :  0.006   0.050   1580
  Dihedral  :  6.625  49.412   1262
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.47 %
    Favored  : 94.14 %
  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: -1.89 (0.23), residues: 1182
  helix: -0.16 (0.18), residues: 782
  sheet: -1.18 (1.02), residues: 20
  loop : -3.61 (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   0.035   0.002   PHE B 306 
 TYR   0.027   0.002   TYR B 146 
 ARG   0.005   0.001   ARG B 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  551)
  hydrogen bonds       : angle       4.66871 ( 1617)
  covalent geometry    : bond        0.00319 ( 9504)
  covalent geometry    : angle       0.77802 (12914)

*********************** 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
  169 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 165
  time to evaluate  : 1.071 
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: 0.9261 (m-10) cc_final: 0.9005 (m-80)
REVERT: B  232 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9307 (pt0)
REVERT: B  246 LEU cc_start: 0.9808 (mm) cc_final: 0.9566 (mt)
REVERT: B  250 MET cc_start: 0.9386 (tpt) cc_final: 0.9097 (ppp)
REVERT: B  339 MET cc_start: 0.9315 (pmm) cc_final: 0.8914 (pmm)
REVERT: B  468 PHE cc_start: 0.9093 (p90) cc_final: 0.8693 (p90)
REVERT: B  490 LEU cc_start: 0.9719 (pp) cc_final: 0.9392 (pp)
REVERT: B  494 PHE cc_start: 0.9323 (m-10) cc_final: 0.9074 (m-80)
REVERT: A  124 LEU cc_start: 0.9754 (tt) cc_final: 0.9421 (tt)
REVERT: A  128 MET cc_start: 0.9576 (mmp) cc_final: 0.9314 (mmm)
REVERT: A  171 LEU cc_start: 0.9806 (mt) cc_final: 0.9547 (tp)
REVERT: A  178 PHE cc_start: 0.9245 (m-10) cc_final: 0.8999 (m-80)
REVERT: A  232 GLU cc_start: 0.9570 (OUTLIER) cc_final: 0.9320 (pt0)
REVERT: A  246 LEU cc_start: 0.9736 (mt) cc_final: 0.9524 (mt)
REVERT: A  250 MET cc_start: 0.9416 (tpt) cc_final: 0.9119 (ppp)
REVERT: A  311 PHE cc_start: 0.9074 (m-80) cc_final: 0.8822 (m-80)
REVERT: A  339 MET cc_start: 0.9306 (pmm) cc_final: 0.8887 (pmm)
REVERT: A  468 PHE cc_start: 0.9117 (p90) cc_final: 0.8805 (p90)
REVERT: A  490 LEU cc_start: 0.9807 (pp) cc_final: 0.9485 (pp)
REVERT: A  494 PHE cc_start: 0.9357 (m-10) cc_final: 0.9077 (m-80)
REVERT: A  532 LEU cc_start: 0.9496 (tp) cc_final: 0.9272 (tp)
REVERT: A  559 MET cc_start: 0.9653 (ptm) cc_final: 0.9329 (ptm)
REVERT: A  653 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9144 (mm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1703
  time to fit residues: 42.4457
Evaluate side-chains
  122 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 101 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.9462

-------------------------------------------------------------------------------
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**
** A 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 = 0.3234 r_free = 0.3234 target = 0.049281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.039241 restraints weight = 72713.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.040385 restraints weight = 49645.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.041255 restraints weight = 37106.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9504  Z= 0.139
  Angle     :  0.758  10.247  12914  Z= 0.384
  Chirality :  0.044   0.150   1526
  Planarity :  0.006   0.050   1580
  Dihedral  :  6.227  48.104   1262
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  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: -1.38 (0.24), residues: 1182
  helix:  0.24 (0.19), residues: 770
  sheet: -0.85 (1.03), residues: 20
  loop : -3.34 (0.26), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 469 
 HIS   0.004   0.001   HIS B 664 
 PHE   0.038   0.002   PHE B 463 
 TYR   0.024   0.002   TYR B 146 
 ARG   0.003   0.000   ARG A 663 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  551)
  hydrogen bonds       : angle       4.44389 ( 1617)
  covalent geometry    : bond        0.00293 ( 9504)
  covalent geometry    : angle       0.75826 (12914)

*********************** 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
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.035 
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: 0.9229 (m-10) cc_final: 0.9022 (m-80)
REVERT: B  246 LEU cc_start: 0.9798 (mm) cc_final: 0.9544 (mt)
REVERT: B  250 MET cc_start: 0.9379 (tpt) cc_final: 0.9095 (ppp)
REVERT: B  339 MET cc_start: 0.9382 (pmm) cc_final: 0.9097 (pmm)
REVERT: B  468 PHE cc_start: 0.9068 (p90) cc_final: 0.8858 (p90)
REVERT: B  490 LEU cc_start: 0.9724 (pp) cc_final: 0.9383 (pp)
REVERT: B  494 PHE cc_start: 0.9227 (m-10) cc_final: 0.8929 (m-80)
REVERT: B  559 MET cc_start: 0.9667 (ptm) cc_final: 0.8884 (ppp)
REVERT: B  560 MET cc_start: 0.9826 (mpp) cc_final: 0.9290 (mpp)
REVERT: B  663 ARG cc_start: 0.7754 (tpm170) cc_final: 0.7384 (tpm170)
REVERT: A  124 LEU cc_start: 0.9656 (tt) cc_final: 0.9220 (tt)
REVERT: A  178 PHE cc_start: 0.9221 (m-10) cc_final: 0.8960 (m-80)
REVERT: A  250 MET cc_start: 0.9437 (tpt) cc_final: 0.9123 (ppp)
REVERT: A  311 PHE cc_start: 0.9071 (m-80) cc_final: 0.8732 (m-80)
REVERT: A  339 MET cc_start: 0.9350 (pmm) cc_final: 0.9084 (pmm)
REVERT: A  345 LEU cc_start: 0.9759 (pp) cc_final: 0.9426 (mt)
REVERT: A  490 LEU cc_start: 0.9777 (pp) cc_final: 0.9482 (pp)
REVERT: A  494 PHE cc_start: 0.9278 (m-10) cc_final: 0.8964 (m-80)
REVERT: A  532 LEU cc_start: 0.9350 (tp) cc_final: 0.9105 (tp)
REVERT: A  559 MET cc_start: 0.9629 (ptm) cc_final: 0.9315 (ptm)
REVERT: A  609 MET cc_start: 0.8616 (pmm) cc_final: 0.8375 (pmm)
REVERT: A  653 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9135 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1714
  time to fit residues: 41.9980
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  : 0.945 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 112 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 45 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.048371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.038627 restraints weight = 75499.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.039775 restraints weight = 50839.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.040631 restraints weight = 37783.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.4144

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= 0.154
  Angle     :  0.775  13.367  12914  Z= 0.391
  Chirality :  0.045   0.241   1526
  Planarity :  0.006   0.048   1580
  Dihedral  :  6.109  46.944   1262
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  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: -1.29 (0.24), residues: 1182
  helix:  0.23 (0.18), residues: 784
  sheet: -0.76 (1.01), residues: 20
  loop : -3.23 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 433 
 HIS   0.003   0.001   HIS B 389 
 PHE   0.034   0.002   PHE A 464 
 TYR   0.025   0.002   TYR B 146 
 ARG   0.003   0.000   ARG A 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 (  551)
  hydrogen bonds       : angle       4.42157 ( 1617)
  covalent geometry    : bond        0.00324 ( 9504)
  covalent geometry    : angle       0.77506 (12914)

*********************** 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  : 1.070 
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: 0.9264 (m-10) cc_final: 0.8935 (m-80)
REVERT: B  209 MET cc_start: 0.9508 (pmm) cc_final: 0.9124 (tmm)
REVERT: B  250 MET cc_start: 0.9434 (tpt) cc_final: 0.9089 (ppp)
REVERT: B  339 MET cc_start: 0.9341 (pmm) cc_final: 0.8931 (pmm)
REVERT: B  468 PHE cc_start: 0.9051 (p90) cc_final: 0.8837 (p90)
REVERT: B  490 LEU cc_start: 0.9721 (pp) cc_final: 0.9383 (pp)
REVERT: B  494 PHE cc_start: 0.9246 (m-10) cc_final: 0.8994 (m-80)
REVERT: B  559 MET cc_start: 0.9674 (ptm) cc_final: 0.8902 (ppp)
REVERT: B  560 MET cc_start: 0.9798 (mpp) cc_final: 0.9264 (mpp)
REVERT: B  663 ARG cc_start: 0.7762 (tpm170) cc_final: 0.7464 (tpm170)
REVERT: A  250 MET cc_start: 0.9441 (tpt) cc_final: 0.9140 (ppp)
REVERT: A  311 PHE cc_start: 0.9081 (m-80) cc_final: 0.8711 (m-80)
REVERT: A  339 MET cc_start: 0.9331 (pmm) cc_final: 0.8845 (pmm)
REVERT: A  461 PHE cc_start: 0.9465 (m-80) cc_final: 0.9238 (m-80)
REVERT: A  468 PHE cc_start: 0.9118 (p90) cc_final: 0.8768 (p90)
REVERT: A  490 LEU cc_start: 0.9768 (pp) cc_final: 0.9448 (pp)
REVERT: A  494 PHE cc_start: 0.9259 (m-10) cc_final: 0.8929 (m-80)
REVERT: A  532 LEU cc_start: 0.9470 (tp) cc_final: 0.9192 (tp)
REVERT: A  559 MET cc_start: 0.9644 (ptm) cc_final: 0.9417 (ptm)
REVERT: A  653 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9101 (mm-30)
REVERT: A  663 ARG cc_start: 0.7888 (tpm170) cc_final: 0.7589 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1706
  time to fit residues: 40.0012
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  : 1.086 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 115 optimal weight:    9.9990
   chunk 107 optimal weight:    0.0770
   chunk 51 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 102 optimal weight:    0.0570
   chunk 113 optimal weight:    0.5980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.050651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.040547 restraints weight = 73024.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.041778 restraints weight = 49523.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.042688 restraints weight = 36684.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.4500

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= 0.137
  Angle     :  0.767  11.074  12914  Z= 0.382
  Chirality :  0.045   0.178   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.918  46.451   1262
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  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: -0.77 (0.24), residues: 1182
  helix:  0.76 (0.19), residues: 748
  sheet: -0.60 (0.98), residues: 20
  loop : -2.98 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 469 
 HIS   0.003   0.001   HIS B 538 
 PHE   0.029   0.002   PHE B 484 
 TYR   0.020   0.001   TYR A 146 
 ARG   0.002   0.000   ARG A 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  551)
  hydrogen bonds       : angle       4.29179 ( 1617)
  covalent geometry    : bond        0.00291 ( 9504)
  covalent geometry    : angle       0.76657 (12914)

*********************** 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
  175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9246 (m-10) cc_final: 0.9009 (m-80)
REVERT: B  209 MET cc_start: 0.9448 (pmm) cc_final: 0.9148 (tmm)
REVERT: B  246 LEU cc_start: 0.9779 (mm) cc_final: 0.9519 (mt)
REVERT: B  250 MET cc_start: 0.9413 (tpt) cc_final: 0.9039 (ppp)
REVERT: B  339 MET cc_start: 0.9340 (pmm) cc_final: 0.8960 (pmm)
REVERT: B  468 PHE cc_start: 0.9033 (p90) cc_final: 0.8590 (p90)
REVERT: B  490 LEU cc_start: 0.9810 (pp) cc_final: 0.9329 (mt)
REVERT: B  494 PHE cc_start: 0.9232 (m-10) cc_final: 0.9029 (m-80)
REVERT: B  547 PHE cc_start: 0.9553 (p90) cc_final: 0.9165 (p90)
REVERT: B  609 MET cc_start: 0.8482 (pmm) cc_final: 0.8108 (pmm)
REVERT: B  663 ARG cc_start: 0.7694 (tpm170) cc_final: 0.7364 (tpm170)
REVERT: A  178 PHE cc_start: 0.9239 (m-10) cc_final: 0.8948 (m-80)
REVERT: A  250 MET cc_start: 0.9462 (tpt) cc_final: 0.9143 (ppp)
REVERT: A  311 PHE cc_start: 0.9102 (m-80) cc_final: 0.8704 (m-80)
REVERT: A  325 ASP cc_start: 0.8049 (m-30) cc_final: 0.7755 (p0)
REVERT: A  339 MET cc_start: 0.9310 (pmm) cc_final: 0.8892 (pmm)
REVERT: A  466 MET cc_start: 0.9355 (tpt) cc_final: 0.9080 (tmm)
REVERT: A  468 PHE cc_start: 0.9125 (p90) cc_final: 0.8897 (p90)
REVERT: A  490 LEU cc_start: 0.9821 (pp) cc_final: 0.9508 (pp)
REVERT: A  494 PHE cc_start: 0.9303 (m-10) cc_final: 0.8966 (m-80)
REVERT: A  527 ILE cc_start: 0.9272 (pt) cc_final: 0.9037 (pt)
REVERT: A  532 LEU cc_start: 0.9181 (tp) cc_final: 0.8892 (tp)
REVERT: A  547 PHE cc_start: 0.9588 (p90) cc_final: 0.9357 (p90)
REVERT: A  609 MET cc_start: 0.8514 (pmm) cc_final: 0.8255 (pmm)
REVERT: A  663 ARG cc_start: 0.7719 (tpm170) cc_final: 0.7417 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1621
  time to fit residues: 42.2354
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  : 0.992 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 13 optimal weight:    0.0040
   chunk 101 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0040
   chunk 90 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.4404

-------------------------------------------------------------------------------
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 = 0.3327 r_free = 0.3327 target = 0.051918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.041692 restraints weight = 70119.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.042938 restraints weight = 46808.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.043872 restraints weight = 34665.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4806

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= 0.140
  Angle     :  0.790  10.831  12914  Z= 0.390
  Chirality :  0.046   0.183   1526
  Planarity :  0.005   0.045   1580
  Dihedral  :  5.807  45.140   1262
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -0.72 (0.24), residues: 1182
  helix:  0.77 (0.19), residues: 746
  sheet: -0.29 (1.02), residues: 20
  loop : -2.91 (0.28), residues: 416

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04138 (  551)
  hydrogen bonds       : angle       4.25220 ( 1617)
  covalent geometry    : bond        0.00298 ( 9504)
  covalent geometry    : angle       0.78980 (12914)

*********************** 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
  173 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.9472 (pmm) cc_final: 0.9164 (tmm)
REVERT: B  461 PHE cc_start: 0.9447 (m-80) cc_final: 0.9244 (m-80)
REVERT: B  468 PHE cc_start: 0.9056 (p90) cc_final: 0.8829 (p90)
REVERT: B  490 LEU cc_start: 0.9829 (pp) cc_final: 0.9553 (pp)
REVERT: B  494 PHE cc_start: 0.9243 (m-10) cc_final: 0.8947 (m-80)
REVERT: B  532 LEU cc_start: 0.9276 (tp) cc_final: 0.9063 (tp)
REVERT: B  547 PHE cc_start: 0.9578 (p90) cc_final: 0.9132 (p90)
REVERT: B  609 MET cc_start: 0.8543 (pmm) cc_final: 0.8173 (pmm)
REVERT: A  178 PHE cc_start: 0.9243 (m-10) cc_final: 0.9042 (m-80)
REVERT: A  250 MET cc_start: 0.9450 (tpt) cc_final: 0.9141 (ppp)
REVERT: A  311 PHE cc_start: 0.9123 (m-80) cc_final: 0.8715 (m-80)
REVERT: A  461 PHE cc_start: 0.9412 (m-80) cc_final: 0.9164 (m-80)
REVERT: A  468 PHE cc_start: 0.9095 (p90) cc_final: 0.8820 (p90)
REVERT: A  470 MET cc_start: 0.9276 (ppp) cc_final: 0.8892 (ppp)
REVERT: A  490 LEU cc_start: 0.9813 (pp) cc_final: 0.9480 (pp)
REVERT: A  494 PHE cc_start: 0.9306 (m-10) cc_final: 0.8984 (m-80)
REVERT: A  532 LEU cc_start: 0.9150 (tp) cc_final: 0.8816 (tp)
REVERT: A  547 PHE cc_start: 0.9614 (p90) cc_final: 0.9357 (p90)
REVERT: A  559 MET cc_start: 0.9685 (ptm) cc_final: 0.8876 (ppp)
REVERT: A  560 MET cc_start: 0.9867 (mpp) cc_final: 0.9261 (mpp)
REVERT: A  609 MET cc_start: 0.8536 (pmm) cc_final: 0.8246 (pmm)
REVERT: A  663 ARG cc_start: 0.7644 (tpm170) cc_final: 0.7324 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1848
  time to fit residues: 47.3016
Evaluate side-chains
  129 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3284 r_free = 0.3284 target = 0.050503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.040706 restraints weight = 74695.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.041898 restraints weight = 50345.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.042777 restraints weight = 37322.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4998

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= 0.156
  Angle     :  0.805  11.171  12914  Z= 0.405
  Chirality :  0.045   0.158   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.824  45.222   1262
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (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: -0.78 (0.24), residues: 1182
  helix:  0.66 (0.19), residues: 758
  sheet: -0.24 (1.00), residues: 20
  loop : -2.88 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 469 
 HIS   0.003   0.001   HIS B 835 
 PHE   0.053   0.003   PHE B 464 
 TYR   0.021   0.002   TYR B 146 
 ARG   0.003   0.000   ARG A 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  551)
  hydrogen bonds       : angle       4.32845 ( 1617)
  covalent geometry    : bond        0.00332 ( 9504)
  covalent geometry    : angle       0.80526 (12914)

*********************** 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
  162 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 LEU cc_start: 0.9641 (tt) cc_final: 0.9431 (mt)
REVERT: B  178 PHE cc_start: 0.9529 (m-80) cc_final: 0.9220 (m-80)
REVERT: B  209 MET cc_start: 0.9473 (pmm) cc_final: 0.9131 (tmm)
REVERT: B  250 MET cc_start: 0.9460 (tpt) cc_final: 0.9078 (ppp)
REVERT: B  468 PHE cc_start: 0.9088 (p90) cc_final: 0.8808 (p90)
REVERT: B  490 LEU cc_start: 0.9827 (pp) cc_final: 0.9545 (pp)
REVERT: B  494 PHE cc_start: 0.9232 (m-10) cc_final: 0.8984 (m-80)
REVERT: B  532 LEU cc_start: 0.9342 (tp) cc_final: 0.9122 (tp)
REVERT: B  547 PHE cc_start: 0.9586 (p90) cc_final: 0.9185 (p90)
REVERT: B  609 MET cc_start: 0.8579 (pmm) cc_final: 0.8292 (pmm)
REVERT: A  178 PHE cc_start: 0.9301 (m-10) cc_final: 0.9072 (m-80)
REVERT: A  250 MET cc_start: 0.9455 (tpt) cc_final: 0.9152 (ppp)
REVERT: A  311 PHE cc_start: 0.9132 (m-80) cc_final: 0.8737 (m-80)
REVERT: A  461 PHE cc_start: 0.9480 (m-80) cc_final: 0.9160 (m-10)
REVERT: A  468 PHE cc_start: 0.9058 (p90) cc_final: 0.8676 (p90)
REVERT: A  490 LEU cc_start: 0.9804 (pp) cc_final: 0.9566 (pp)
REVERT: A  494 PHE cc_start: 0.9271 (m-10) cc_final: 0.9001 (m-80)
REVERT: A  532 LEU cc_start: 0.9283 (tp) cc_final: 0.8949 (tp)
REVERT: A  547 PHE cc_start: 0.9589 (p90) cc_final: 0.9246 (p90)
REVERT: A  559 MET cc_start: 0.9680 (ptm) cc_final: 0.9394 (ptm)
REVERT: A  609 MET cc_start: 0.8682 (pmm) cc_final: 0.8440 (pmm)
REVERT: A  663 ARG cc_start: 0.7642 (tpm170) cc_final: 0.7327 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1739
  time to fit residues: 42.0795
Evaluate side-chains
  125 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 107 optimal weight:    8.9990
   chunk 81 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.050282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.038998 restraints weight = 76911.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.040320 restraints weight = 49260.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.041301 restraints weight = 35641.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.5205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9504  Z= 0.168
  Angle     :  0.812  12.615  12914  Z= 0.410
  Chirality :  0.045   0.155   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.859  44.748   1262
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  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: -0.77 (0.24), residues: 1182
  helix:  0.61 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -2.66 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 469 
 HIS   0.013   0.001   HIS B 847 
 PHE   0.053   0.002   PHE B 464 
 TYR   0.018   0.002   TYR B 146 
 ARG   0.004   0.000   ARG B 669 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  551)
  hydrogen bonds       : angle       4.38700 ( 1617)
  covalent geometry    : bond        0.00356 ( 9504)
  covalent geometry    : angle       0.81238 (12914)

*********************** 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
  157 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.9485 (pmm) cc_final: 0.9133 (tmm)
REVERT: B  246 LEU cc_start: 0.9807 (mm) cc_final: 0.9566 (mt)
REVERT: B  250 MET cc_start: 0.9462 (tpt) cc_final: 0.9097 (ppp)
REVERT: B  468 PHE cc_start: 0.9132 (p90) cc_final: 0.8904 (p90)
REVERT: B  490 LEU cc_start: 0.9807 (pp) cc_final: 0.9510 (pp)
REVERT: B  494 PHE cc_start: 0.9210 (m-10) cc_final: 0.8957 (m-80)
REVERT: B  559 MET cc_start: 0.9740 (ptm) cc_final: 0.9349 (ptp)
REVERT: A  178 PHE cc_start: 0.9328 (m-10) cc_final: 0.9083 (m-80)
REVERT: A  250 MET cc_start: 0.9484 (tpt) cc_final: 0.9132 (ppp)
REVERT: A  311 PHE cc_start: 0.9118 (m-80) cc_final: 0.8765 (m-80)
REVERT: A  461 PHE cc_start: 0.9482 (m-80) cc_final: 0.9244 (m-80)
REVERT: A  468 PHE cc_start: 0.9085 (p90) cc_final: 0.8662 (p90)
REVERT: A  490 LEU cc_start: 0.9763 (pp) cc_final: 0.9498 (pp)
REVERT: A  494 PHE cc_start: 0.9203 (m-10) cc_final: 0.8942 (m-80)
REVERT: A  532 LEU cc_start: 0.9385 (tp) cc_final: 0.9042 (tp)
REVERT: A  559 MET cc_start: 0.9715 (ptm) cc_final: 0.9386 (ptm)
REVERT: A  663 ARG cc_start: 0.7673 (tpm170) cc_final: 0.7369 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1709
  time to fit residues: 40.0104
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  : 1.049 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 84 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   chunk 101 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0770
   overall best weight:    0.7540

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.051973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.040226 restraints weight = 75330.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.041629 restraints weight = 47860.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.042688 restraints weight = 34265.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.5430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9504  Z= 0.142
  Angle     :  0.802  11.803  12914  Z= 0.400
  Chirality :  0.046   0.155   1526
  Planarity :  0.005   0.046   1580
  Dihedral  :  5.688  45.759   1262
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  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: -0.61 (0.24), residues: 1182
  helix:  0.77 (0.19), residues: 758
  sheet: -0.27 (0.93), residues: 20
  loop : -2.77 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 469 
 HIS   0.007   0.001   HIS B 847 
 PHE   0.049   0.002   PHE B 464 
 TYR   0.014   0.001   TYR A 146 
 ARG   0.001   0.000   ARG B 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  551)
  hydrogen bonds       : angle       4.34672 ( 1617)
  covalent geometry    : bond        0.00302 ( 9504)
  covalent geometry    : angle       0.80209 (12914)

********************** 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
  168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.9537 (m-80) cc_final: 0.9215 (m-80)
REVERT: B  209 MET cc_start: 0.9497 (pmm) cc_final: 0.9144 (tmm)
REVERT: B  246 LEU cc_start: 0.9804 (mm) cc_final: 0.9569 (mt)
REVERT: B  250 MET cc_start: 0.9489 (tpt) cc_final: 0.9136 (ppp)
REVERT: B  468 PHE cc_start: 0.9107 (p90) cc_final: 0.8725 (p90)
REVERT: B  490 LEU cc_start: 0.9811 (pp) cc_final: 0.9488 (pp)
REVERT: B  494 PHE cc_start: 0.9194 (m-10) cc_final: 0.8907 (m-80)
REVERT: B  532 LEU cc_start: 0.9342 (tp) cc_final: 0.9134 (tp)
REVERT: B  547 PHE cc_start: 0.9593 (p90) cc_final: 0.9141 (p90)
REVERT: B  559 MET cc_start: 0.9750 (ptm) cc_final: 0.9530 (ptm)
REVERT: A  250 MET cc_start: 0.9514 (tpt) cc_final: 0.9170 (ppp)
REVERT: A  311 PHE cc_start: 0.9115 (m-80) cc_final: 0.8625 (m-80)
REVERT: A  461 PHE cc_start: 0.9423 (m-80) cc_final: 0.9198 (m-80)
REVERT: A  464 PHE cc_start: 0.9034 (p90) cc_final: 0.8634 (p90)
REVERT: A  468 PHE cc_start: 0.9037 (p90) cc_final: 0.8602 (p90)
REVERT: A  490 LEU cc_start: 0.9773 (pp) cc_final: 0.9500 (pp)
REVERT: A  494 PHE cc_start: 0.9251 (m-10) cc_final: 0.8916 (m-80)
REVERT: A  532 LEU cc_start: 0.9306 (tp) cc_final: 0.9038 (tp)
REVERT: A  559 MET cc_start: 0.9765 (ptm) cc_final: 0.9343 (ptp)
REVERT: A  663 ARG cc_start: 0.7678 (tpm170) cc_final: 0.7046 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1771
  time to fit residues: 44.1489
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  : 1.068 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 114 optimal weight:    9.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.051715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.040036 restraints weight = 75041.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.041406 restraints weight = 48126.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.042431 restraints weight = 34735.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.5541

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= 0.142
  Angle     :  0.788  10.299  12914  Z= 0.393
  Chirality :  0.045   0.159   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.617  45.796   1262
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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: -0.57 (0.24), residues: 1182
  helix:  0.77 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -2.59 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 469 
 HIS   0.006   0.001   HIS B 847 
 PHE   0.035   0.002   PHE B 306 
 TYR   0.015   0.001   TYR B 146 
 ARG   0.002   0.000   ARG B 669 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  551)
  hydrogen bonds       : angle       4.26383 ( 1617)
  covalent geometry    : bond        0.00304 ( 9504)
  covalent geometry    : angle       0.78818 (12914)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3079.91 seconds
wall clock time: 54 minutes 11.30 seconds (3251.30 seconds total)