Starting phenix.real_space_refine
on Wed Mar  4 20:58:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vqu_21357/03_2026/6vqu_21357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vqu_21357/03_2026/6vqu_21357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vqu_21357/03_2026/6vqu_21357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vqu_21357/03_2026/6vqu_21357.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vqu_21357/03_2026/6vqu_21357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vqu_21357/03_2026/6vqu_21357.map"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8895 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5846      2.51       5
     N    1624      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9156
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4578
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 15, 'TRANS': 573}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.43, per 1000 atoms: 0.37
  Number of scatterers: 9156
  At special positions: 0
  Unit cell: (110.922, 86.736, 140.946, 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      24     16.00
     O    1662      8.00
     N    1624      7.00
     C    5846      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 435.7 milliseconds
  

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      73.5% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 28
      Proline residue:  A  25  - end of helix
    Processing helix  chain 'A' and resid 32 through 69
      Proline residue:  A  57  - end of helix
    Processing helix  chain 'A' and resid 75 through 127
      removed outlier: 4.534A  pdb=" N   ARG A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   VAL A 108 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 135
      removed outlier: 3.878A  pdb=" N   HIS A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 161
    Processing helix  chain 'A' and resid 161 through 178
    Processing helix  chain 'A' and resid 181 through 230
      removed outlier: 3.962A  pdb=" N   VAL A 185 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 238
    Processing helix  chain 'A' and resid 239 through 293
    Processing helix  chain 'A' and resid 298 through 312
      removed outlier: 4.021A  pdb=" N   VAL A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.929A  pdb=" N   ASP A 316 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 317 through 341
    Processing helix  chain 'A' and resid 401 through 408
      removed outlier: 4.535A  pdb=" N   ARG A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 428
      No H-bonds generated for 'chain 'A' and resid 426 through 428'
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 450 through 456
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 463 through 474
    Processing helix  chain 'A' and resid 476 through 483
    Processing helix  chain 'A' and resid 485 through 489
      removed outlier: 3.546A  pdb=" N   THR A 489 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 529 through 544
      removed outlier: 4.389A  pdb=" N   SER A 538 " --> pdb=" O   GLN A 534 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 539 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 587 through 602
    Processing helix  chain 'B' and resid 15 through 28
      Proline residue:  B  25  - end of helix
    Processing helix  chain 'B' and resid 32 through 69
      Proline residue:  B  57  - end of helix
    Processing helix  chain 'B' and resid 75 through 127
      removed outlier: 4.533A  pdb=" N   ARG B 107 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   VAL B 108 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 135
      removed outlier: 3.879A  pdb=" N   HIS B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 161
    Processing helix  chain 'B' and resid 161 through 178
    Processing helix  chain 'B' and resid 181 through 230
      removed outlier: 3.962A  pdb=" N   VAL B 185 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 238
    Processing helix  chain 'B' and resid 239 through 293
    Processing helix  chain 'B' and resid 298 through 312
      removed outlier: 4.020A  pdb=" N   VAL B 302 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 316
      removed outlier: 3.928A  pdb=" N   ASP B 316 " --> pdb=" O   ARG B 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 313 through 316'
    Processing helix  chain 'B' and resid 317 through 341
    Processing helix  chain 'B' and resid 401 through 408
      removed outlier: 4.535A  pdb=" N   ARG B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 428
      No H-bonds generated for 'chain 'B' and resid 426 through 428'
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 450 through 456
    Processing helix  chain 'B' and resid 457 through 459
      No H-bonds generated for 'chain 'B' and resid 457 through 459'
    Processing helix  chain 'B' and resid 463 through 474
    Processing helix  chain 'B' and resid 476 through 483
    Processing helix  chain 'B' and resid 485 through 489
      removed outlier: 3.546A  pdb=" N   THR B 489 " --> pdb=" O   GLY B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 515
    Processing helix  chain 'B' and resid 529 through 544
      removed outlier: 4.389A  pdb=" N   SER B 538 " --> pdb=" O   GLN B 534 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   THR B 539 " --> pdb=" O   ASP B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 578 through 586
    Processing helix  chain 'B' and resid 587 through 602
    Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 384
      removed outlier: 4.166A  pdb=" N   GLY A 379 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   VAL A 366 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   SER A 381 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASP A 364 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   GLU A 383 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR A 362 " --> pdb=" O   GLU A 383 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   PHE A 363 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU A 419 " --> pdb=" O   PHE A 363 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ASN A 365 " --> pdb=" O   ARG A 417 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ARG A 417 " --> pdb=" O   ASN A 365 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 440
      removed outlier: 6.724A  pdb=" N   GLY A 438 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   ASP A 522 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL A 440 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   LEU A 519 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   PHE A 521 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG A 389 " --> pdb=" O   THR A 564 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   LEU A 566 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU A 568 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL A 393 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP A 569 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   LEU A 573 " --> pdb=" O   ASP A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 384
      removed outlier: 4.166A  pdb=" N   GLY B 379 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   VAL B 366 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   SER B 381 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ASP B 364 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   GLU B 383 " --> pdb=" O   THR B 362 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR B 362 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   PHE B 363 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU B 419 " --> pdb=" O   PHE B 363 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ASN B 365 " --> pdb=" O   ARG B 417 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ARG B 417 " --> pdb=" O   ASN B 365 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 440
      removed outlier: 6.725A  pdb=" N   GLY B 438 " --> pdb=" O   LEU B 520 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ASP B 522 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL B 440 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   LEU B 519 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ILE B 552 " --> pdb=" O   LEU B 519 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   PHE B 521 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG B 389 " --> pdb=" O   THR B 564 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   LEU B 566 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA B 391 " --> pdb=" O   LEU B 566 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU B 568 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL B 393 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP B 569 " --> pdb=" O   LEU B 573 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   LEU B 573 " --> pdb=" O   ASP B 569 " (cutoff:3.500A)

    668 hydrogen bonds defined for protein.
    1962 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 0.92 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: 2965
        1.34 -     1.45: 1418
        1.45 -     1.57: 4895
        1.57 -     1.69: 0
        1.69 -     1.80: 48
  Bond restraints: 9326
  Sorted by residual:
  bond pdb=" CB  PRO B  57 "
       pdb=" CG  PRO B  57 "
    ideal  model  delta    sigma   weight residual
    1.492  1.384  0.108 5.00e-02 4.00e+02 4.68e+00
  bond pdb=" CB  PRO A  57 "
       pdb=" CG  PRO A  57 "
    ideal  model  delta    sigma   weight residual
    1.492  1.384  0.108 5.00e-02 4.00e+02 4.66e+00
  bond pdb=" C   GLN B  74 "
       pdb=" N   PRO B  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.048 2.34e-02 1.83e+03 4.13e+00
  bond pdb=" C   GLN A  74 "
       pdb=" N   PRO A  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.08e+00
  bond pdb=" CA  LEU A  56 "
       pdb=" C   LEU A  56 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 1.26e-02 6.30e+03 3.47e+00
  ... (remaining 9321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 11912
        1.76 -     3.51: 618
        3.51 -     5.27: 107
        5.27 -     7.02: 19
        7.02 -     8.78: 12
  Bond angle restraints: 12668
  Sorted by residual:
  angle pdb=" CA  ARG A 494 "
        pdb=" CB  ARG A 494 "
        pdb=" CG  ARG A 494 "
      ideal   model   delta    sigma   weight residual
     114.10  121.37   -7.27 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" CA  ARG B 494 "
        pdb=" CB  ARG B 494 "
        pdb=" CG  ARG B 494 "
      ideal   model   delta    sigma   weight residual
     114.10  121.36   -7.26 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" C   ASP B 569 "
        pdb=" N   GLN B 570 "
        pdb=" CA  GLN B 570 "
      ideal   model   delta    sigma   weight residual
     122.46  127.56   -5.10 1.41e+00 5.03e-01 1.31e+01
  angle pdb=" C   ASP A 569 "
        pdb=" N   GLN A 570 "
        pdb=" CA  GLN A 570 "
      ideal   model   delta    sigma   weight residual
     122.46  127.49   -5.03 1.41e+00 5.03e-01 1.27e+01
  angle pdb=" C   GLU B 493 "
        pdb=" N   ARG B 494 "
        pdb=" CA  ARG B 494 "
      ideal   model   delta    sigma   weight residual
     122.08  127.09   -5.01 1.47e+00 4.63e-01 1.16e+01
  ... (remaining 12663 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.89: 4673
       13.89 -    27.78: 621
       27.78 -    41.66: 174
       41.66 -    55.55: 50
       55.55 -    69.44: 18
  Dihedral angle restraints: 5536
    sinusoidal: 2140
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CA  PHE A 368 "
           pdb=" C   PHE A 368 "
           pdb=" N   GLY A 369 "
           pdb=" CA  GLY A 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.61   26.39     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  PHE B 368 "
           pdb=" C   PHE B 368 "
           pdb=" N   GLY B 369 "
           pdb=" CA  GLY B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.70   26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  ALA A  76 "
           pdb=" C   ALA A  76 "
           pdb=" N   LEU A  77 "
           pdb=" CA  LEU A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.89   20.11     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 5533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1079
       0.053 -    0.106: 279
       0.106 -    0.160: 111
       0.160 -    0.213: 9
       0.213 -    0.266: 6
  Chirality restraints: 1484
  Sorted by residual:
  chirality pdb=" CB  VAL B 543 "
            pdb=" CA  VAL B 543 "
            pdb=" CG1 VAL B 543 "
            pdb=" CG2 VAL B 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  VAL A 543 "
            pdb=" CA  VAL A 543 "
            pdb=" CG1 VAL A 543 "
            pdb=" CG2 VAL A 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  ILE A 559 "
            pdb=" CA  ILE A 559 "
            pdb=" CG1 ILE A 559 "
            pdb=" CG2 ILE A 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1481 not shown)

  Planarity restraints: 1616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 543 "    0.018 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   VAL A 543 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   VAL A 543 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA A 544 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 543 "   -0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   VAL B 543 "    0.062 2.00e-02 2.50e+03
        pdb=" O   VAL B 543 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B 544 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 303 "    0.024 2.00e-02 2.50e+03   1.70e-02 5.03e+00
        pdb=" CG  PHE A 303 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 303 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 303 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 303 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1613 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2554
        2.80 -     3.33: 9066
        3.33 -     3.85: 15907
        3.85 -     4.38: 17055
        4.38 -     4.90: 28934
  Nonbonded interactions: 73516
  Sorted by model distance:
  nonbonded pdb=" O   THR A 199 "
            pdb=" OG1 THR A 203 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   THR B 199 "
            pdb=" OG1 THR B 203 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR B 429 "
            pdb=" OG  SER B 432 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASP B  15 "
            pdb=" OG1 THR B  19 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASP A  15 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.293 3.040
  ... (remaining 73511 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain '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:             4.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.960
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
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      :  0.007   0.108   9326  Z= 0.305
  Angle     :  0.942   8.779  12668  Z= 0.539
  Chirality :  0.056   0.266   1484
  Planarity :  0.007   0.054   1616
  Dihedral  : 14.622  69.440   3352
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.09 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.21), residues: 1174
  helix: -1.29 (0.15), residues: 788
  sheet: -1.53 (0.62), residues: 72
  loop : -1.51 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 434 
 TYR   0.018   0.003   TYR A  60 
 PHE   0.035   0.003   PHE B 303 
 TRP   0.015   0.002   TRP B  28 
 HIS   0.005   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 ( 9326)
  covalent geometry    : angle       0.94161 (12668)
  hydrogen bonds       : bond        0.11070 (  668)
  hydrogen bonds       : angle       5.20409 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9434 (tmm) cc_final: 0.9034 (tmm)
REVERT: A  592 MET cc_start: 0.9194 (mtp) cc_final: 0.8904 (mtp)
REVERT: B  154 MET cc_start: 0.9437 (tmm) cc_final: 0.9125 (tmm)
REVERT: B  592 MET cc_start: 0.9240 (mtp) cc_final: 0.8992 (mtp)
  outliers start: 16
  outliers final: 2
  residues processed: 74
  average time/residue: 0.1341
  time to fit residues: 13.1161
Evaluate side-chains
  41 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  543 VAL
Chi-restraints excluded: chain B residue  543 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
B  14 HIS
B 119 ASN
B 125 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.034747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.026175 restraints weight = 83944.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.027030 restraints weight = 51053.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.027652 restraints weight = 37095.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.028078 restraints weight = 29593.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.028380 restraints weight = 25179.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9326  Z= 0.132
  Angle     :  0.585   7.531  12668  Z= 0.308
  Chirality :  0.040   0.148   1484
  Planarity :  0.005   0.128   1616
  Dihedral  :  4.188  20.431   1308
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.49 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.23), residues: 1174
  helix:  0.76 (0.17), residues: 794
  sheet: -1.37 (0.61), residues: 70
  loop : -0.89 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 146 
 TYR   0.011   0.001   TYR A 589 
 PHE   0.016   0.001   PHE B 303 
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9326)
  covalent geometry    : angle       0.58477 (12668)
  hydrogen bonds       : bond        0.05643 (  668)
  hydrogen bonds       : angle       4.08132 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9738 (tmm) cc_final: 0.9360 (tmm)
REVERT: A  320 MET cc_start: 0.9673 (ptp) cc_final: 0.9174 (pmm)
REVERT: A  592 MET cc_start: 0.9397 (mtp) cc_final: 0.9113 (mtp)
REVERT: B   45 MET cc_start: 0.9640 (mmp) cc_final: 0.8878 (tpp)
REVERT: B  154 MET cc_start: 0.9729 (tmm) cc_final: 0.9405 (tmm)
REVERT: B  320 MET cc_start: 0.9690 (ptp) cc_final: 0.9363 (pmm)
REVERT: B  335 MET cc_start: 0.9460 (mpp) cc_final: 0.9186 (mpp)
REVERT: B  592 MET cc_start: 0.9475 (mtp) cc_final: 0.9221 (mtp)
  outliers start: 17
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0842
  time to fit residues: 7.8513
Evaluate side-chains
  41 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  362 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 114 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
B 119 ASN
B 125 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.034938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.026484 restraints weight = 83503.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.027337 restraints weight = 51216.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.027950 restraints weight = 37075.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.028382 restraints weight = 29543.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.028667 restraints weight = 25109.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9326  Z= 0.123
  Angle     :  0.540   7.386  12668  Z= 0.283
  Chirality :  0.039   0.141   1484
  Planarity :  0.003   0.038   1616
  Dihedral  :  3.864  21.783   1306
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.62 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.24), residues: 1174
  helix:  1.55 (0.18), residues: 800
  sheet: -1.36 (0.60), residues: 70
  loop : -0.47 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 146 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.025   0.001   PHE A 105 
 TRP   0.009   0.001   TRP A 291 
 HIS   0.003   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9326)
  covalent geometry    : angle       0.53999 (12668)
  hydrogen bonds       : bond        0.05097 (  668)
  hydrogen bonds       : angle       3.85821 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9681 (tmm) cc_final: 0.9347 (tmm)
REVERT: A  159 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9319 (tt)
REVERT: A  320 MET cc_start: 0.9691 (ptp) cc_final: 0.9223 (pmm)
REVERT: A  592 MET cc_start: 0.9383 (mtp) cc_final: 0.9094 (mtp)
REVERT: B  125 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.9034 (m-70)
REVERT: B  154 MET cc_start: 0.9690 (tmm) cc_final: 0.9409 (tmm)
REVERT: B  159 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9328 (tt)
REVERT: B  320 MET cc_start: 0.9686 (ptp) cc_final: 0.9224 (pmm)
REVERT: B  335 MET cc_start: 0.9417 (mpp) cc_final: 0.9134 (mpp)
REVERT: B  592 MET cc_start: 0.9450 (mtp) cc_final: 0.9185 (mtp)
  outliers start: 15
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0979
  time to fit residues: 8.0037
Evaluate side-chains
  44 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  362 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
B 119 ASN
B 125 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.034930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026527 restraints weight = 84967.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.027411 restraints weight = 51551.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.028034 restraints weight = 37049.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.028472 restraints weight = 29316.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.028782 restraints weight = 24854.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9326  Z= 0.122
  Angle     :  0.533   9.717  12668  Z= 0.277
  Chirality :  0.039   0.165   1484
  Planarity :  0.003   0.037   1616
  Dihedral  :  3.761  22.564   1306
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.06 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.24), residues: 1174
  helix:  1.85 (0.18), residues: 800
  sheet: -1.33 (0.60), residues: 70
  loop : -0.28 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 531 
 TYR   0.010   0.001   TYR A 195 
 PHE   0.025   0.001   PHE A 105 
 TRP   0.011   0.001   TRP B 291 
 HIS   0.013   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9326)
  covalent geometry    : angle       0.53324 (12668)
  hydrogen bonds       : bond        0.04814 (  668)
  hydrogen bonds       : angle       3.79776 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 33
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.9594 (mmp) cc_final: 0.9340 (mtp)
REVERT: A  154 MET cc_start: 0.9708 (tmm) cc_final: 0.9328 (tmm)
REVERT: A  159 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9261 (tt)
REVERT: A  320 MET cc_start: 0.9666 (ptp) cc_final: 0.9251 (pmm)
REVERT: A  332 MET cc_start: 0.9304 (ttt) cc_final: 0.9028 (tpp)
REVERT: A  592 MET cc_start: 0.9361 (mtp) cc_final: 0.9072 (mtp)
REVERT: B  154 MET cc_start: 0.9708 (tmm) cc_final: 0.9404 (tmm)
REVERT: B  159 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9350 (tt)
REVERT: B  320 MET cc_start: 0.9655 (ptp) cc_final: 0.9223 (pmm)
REVERT: B  592 MET cc_start: 0.9440 (mtp) cc_final: 0.9169 (mtp)
  outliers start: 15
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0705
  time to fit residues: 5.6330
Evaluate side-chains
  43 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  362 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 93 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0870
   chunk 113 optimal weight:    8.9990
   overall best weight:    1.1560

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
B 119 ASN
B 125 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.034789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026340 restraints weight = 84875.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.027219 restraints weight = 51478.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.027849 restraints weight = 36954.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.028290 restraints weight = 29318.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.028584 restraints weight = 24853.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9326  Z= 0.123
  Angle     :  0.525   9.800  12668  Z= 0.272
  Chirality :  0.039   0.167   1484
  Planarity :  0.003   0.032   1616
  Dihedral  :  3.669  22.402   1306
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.85 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.24), residues: 1174
  helix:  2.06 (0.18), residues: 800
  sheet: -1.18 (0.60), residues: 70
  loop : -0.09 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 541 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.027   0.001   PHE B 105 
 TRP   0.008   0.001   TRP A  17 
 HIS   0.002   0.000   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9326)
  covalent geometry    : angle       0.52453 (12668)
  hydrogen bonds       : bond        0.04631 (  668)
  hydrogen bonds       : angle       3.75954 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9695 (tmm) cc_final: 0.9382 (tmm)
REVERT: A  159 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9393 (tt)
REVERT: A  213 MET cc_start: 0.9460 (ppp) cc_final: 0.9260 (ppp)
REVERT: A  280 MET cc_start: 0.9403 (ttp) cc_final: 0.9068 (tpp)
REVERT: A  320 MET cc_start: 0.9662 (ptp) cc_final: 0.9347 (pmm)
REVERT: A  592 MET cc_start: 0.9364 (mtp) cc_final: 0.9075 (mtp)
REVERT: B   45 MET cc_start: 0.9582 (mmp) cc_final: 0.9289 (mtm)
REVERT: B  154 MET cc_start: 0.9698 (tmm) cc_final: 0.9390 (tmm)
REVERT: B  159 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9344 (tt)
REVERT: B  320 MET cc_start: 0.9621 (ptp) cc_final: 0.9181 (pmm)
REVERT: B  592 MET cc_start: 0.9441 (mtp) cc_final: 0.9175 (mtp)
  outliers start: 24
  outliers final: 13
  residues processed: 56
  average time/residue: 0.0762
  time to fit residues: 6.7885
Evaluate side-chains
  48 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 33
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  433 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 115 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 96 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   chunk 99 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
B 125 HIS
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.034130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.025701 restraints weight = 84930.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026554 restraints weight = 51812.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.027159 restraints weight = 37394.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.027585 restraints weight = 29871.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.027881 restraints weight = 25446.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9326  Z= 0.148
  Angle     :  0.555  10.891  12668  Z= 0.287
  Chirality :  0.040   0.166   1484
  Planarity :  0.003   0.031   1616
  Dihedral  :  3.717  23.730   1306
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.91 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.25), residues: 1174
  helix:  2.18 (0.18), residues: 800
  sheet: -1.16 (0.60), residues: 70
  loop :  0.06 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 541 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.024   0.001   PHE B 105 
 TRP   0.010   0.001   TRP A  17 
 HIS   0.002   0.001   HIS B 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9326)
  covalent geometry    : angle       0.55531 (12668)
  hydrogen bonds       : bond        0.04740 (  668)
  hydrogen bonds       : angle       3.82616 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 32
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.9608 (mmp) cc_final: 0.9316 (mtp)
REVERT: A  154 MET cc_start: 0.9702 (tmm) cc_final: 0.9392 (tmm)
REVERT: A  159 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9402 (tt)
REVERT: A  213 MET cc_start: 0.9488 (ppp) cc_final: 0.9286 (ppp)
REVERT: A  280 MET cc_start: 0.9405 (ttp) cc_final: 0.9014 (tpp)
REVERT: A  320 MET cc_start: 0.9642 (ptp) cc_final: 0.9377 (pmm)
REVERT: A  433 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9426 (pp)
REVERT: A  592 MET cc_start: 0.9366 (mtp) cc_final: 0.9065 (mtp)
REVERT: B  154 MET cc_start: 0.9702 (tmm) cc_final: 0.9433 (tmm)
REVERT: B  159 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9398 (tt)
REVERT: B  433 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9454 (pp)
REVERT: B  592 MET cc_start: 0.9432 (mtp) cc_final: 0.9135 (mtp)
  outliers start: 26
  outliers final: 14
  residues processed: 56
  average time/residue: 0.0857
  time to fit residues: 7.4571
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 31
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  433 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 64 optimal weight:    0.5980
   chunk 113 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.034610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026114 restraints weight = 84242.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.026987 restraints weight = 51533.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.027597 restraints weight = 37250.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.028024 restraints weight = 29781.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.028325 restraints weight = 25437.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9326  Z= 0.119
  Angle     :  0.542  10.353  12668  Z= 0.279
  Chirality :  0.040   0.186   1484
  Planarity :  0.003   0.041   1616
  Dihedral  :  3.656  23.101   1306
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.06 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.25), residues: 1174
  helix:  2.24 (0.18), residues: 800
  sheet: -1.10 (0.61), residues: 70
  loop :  0.12 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 531 
 TYR   0.010   0.001   TYR A 195 
 PHE   0.019   0.001   PHE B 105 
 TRP   0.007   0.001   TRP A  17 
 HIS   0.002   0.000   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9326)
  covalent geometry    : angle       0.54201 (12668)
  hydrogen bonds       : bond        0.04596 (  668)
  hydrogen bonds       : angle       3.73566 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 32
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9691 (tmm) cc_final: 0.9385 (tmm)
REVERT: A  159 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9462 (tt)
REVERT: A  280 MET cc_start: 0.9369 (ttp) cc_final: 0.8965 (tpp)
REVERT: A  320 MET cc_start: 0.9625 (ptp) cc_final: 0.9373 (pmm)
REVERT: A  433 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9407 (pp)
REVERT: A  592 MET cc_start: 0.9370 (mtp) cc_final: 0.9062 (mtp)
REVERT: B   45 MET cc_start: 0.9568 (mmp) cc_final: 0.9228 (mtm)
REVERT: B  154 MET cc_start: 0.9693 (tmm) cc_final: 0.9424 (tmm)
REVERT: B  159 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9383 (tt)
REVERT: B  592 MET cc_start: 0.9431 (mtp) cc_final: 0.9132 (mtp)
  outliers start: 32
  outliers final: 16
  residues processed: 62
  average time/residue: 0.0685
  time to fit residues: 7.1375
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 30
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  433 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0770
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.035144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.026593 restraints weight = 82852.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027462 restraints weight = 51334.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.028067 restraints weight = 37320.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.028515 restraints weight = 29885.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.028819 restraints weight = 25485.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9326  Z= 0.112
  Angle     :  0.589  13.398  12668  Z= 0.288
  Chirality :  0.040   0.206   1484
  Planarity :  0.003   0.032   1616
  Dihedral  :  3.590  22.209   1306
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.45 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.24), residues: 1174
  helix:  2.25 (0.18), residues: 800
  sheet: -1.05 (0.61), residues: 70
  loop :  0.11 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 531 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.015   0.001   PHE B 105 
 TRP   0.011   0.001   TRP B 291 
 HIS   0.002   0.000   HIS B 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 9326)
  covalent geometry    : angle       0.58851 (12668)
  hydrogen bonds       : bond        0.04490 (  668)
  hydrogen bonds       : angle       3.72818 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 33
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9679 (tmm) cc_final: 0.9367 (tmm)
REVERT: A  159 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9454 (tt)
REVERT: A  280 MET cc_start: 0.9340 (ttp) cc_final: 0.8969 (tpp)
REVERT: A  320 MET cc_start: 0.9603 (ptp) cc_final: 0.9359 (pmm)
REVERT: A  335 MET cc_start: 0.9379 (mpp) cc_final: 0.9075 (mpp)
REVERT: A  592 MET cc_start: 0.9343 (mtp) cc_final: 0.9037 (mtp)
REVERT: B   45 MET cc_start: 0.9569 (mmp) cc_final: 0.9268 (mtm)
REVERT: B  154 MET cc_start: 0.9687 (tmm) cc_final: 0.9414 (tmm)
REVERT: B  159 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9391 (tt)
REVERT: B  592 MET cc_start: 0.9423 (mtp) cc_final: 0.9120 (mtp)
  outliers start: 21
  outliers final: 17
  residues processed: 52
  average time/residue: 0.0688
  time to fit residues: 6.0599
Evaluate side-chains
  50 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 31
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  433 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0470
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    1.3682

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

Flipped N/Q/H residues before XYZ refinement:
B 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.034670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.026161 restraints weight = 84018.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.027020 restraints weight = 51904.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.027620 restraints weight = 37746.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.028020 restraints weight = 30246.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.028333 restraints weight = 26047.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9326  Z= 0.130
  Angle     :  0.587  11.720  12668  Z= 0.295
  Chirality :  0.040   0.205   1484
  Planarity :  0.003   0.031   1616
  Dihedral  :  3.599  22.566   1306
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.87 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.24), residues: 1174
  helix:  2.28 (0.18), residues: 800
  sheet: -1.03 (0.61), residues: 70
  loop :  0.15 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 531 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.013   0.001   PHE B 105 
 TRP   0.009   0.001   TRP B 291 
 HIS   0.002   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9326)
  covalent geometry    : angle       0.58675 (12668)
  hydrogen bonds       : bond        0.04468 (  668)
  hydrogen bonds       : angle       3.79739 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 33
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9679 (tmm) cc_final: 0.9372 (tmm)
REVERT: A  159 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9475 (tt)
REVERT: A  280 MET cc_start: 0.9368 (ttp) cc_final: 0.8994 (tpp)
REVERT: A  320 MET cc_start: 0.9613 (ptp) cc_final: 0.9364 (pmm)
REVERT: A  335 MET cc_start: 0.9346 (mpp) cc_final: 0.8874 (mtm)
REVERT: A  433 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9426 (pp)
REVERT: A  592 MET cc_start: 0.9329 (mtp) cc_final: 0.9025 (mtp)
REVERT: B   45 MET cc_start: 0.9562 (mmp) cc_final: 0.9280 (mtp)
REVERT: B   67 MET cc_start: 0.9563 (tpp) cc_final: 0.9354 (tpp)
REVERT: B  154 MET cc_start: 0.9692 (tmm) cc_final: 0.9415 (tmm)
REVERT: B  159 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9401 (tt)
REVERT: B  592 MET cc_start: 0.9422 (mtp) cc_final: 0.9114 (mtp)
  outliers start: 21
  outliers final: 16
  residues processed: 52
  average time/residue: 0.0672
  time to fit residues: 5.9210
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 30
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  433 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0000
   chunk 64 optimal weight:    0.0030
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.3998

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

Flipped N/Q/H residues before XYZ refinement:
B 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.034538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.026009 restraints weight = 84238.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.026856 restraints weight = 52092.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027462 restraints weight = 37993.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.027886 restraints weight = 30497.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.028177 restraints weight = 26055.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9326  Z= 0.133
  Angle     :  0.595  12.029  12668  Z= 0.301
  Chirality :  0.041   0.205   1484
  Planarity :  0.003   0.031   1616
  Dihedral  :  3.613  22.915   1306
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.09 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.24), residues: 1174
  helix:  2.26 (0.18), residues: 800
  sheet: -1.02 (0.61), residues: 72
  loop :  0.18 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 531 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.013   0.001   PHE B 105 
 TRP   0.008   0.001   TRP A 291 
 HIS   0.003   0.000   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9326)
  covalent geometry    : angle       0.59496 (12668)
  hydrogen bonds       : bond        0.04502 (  668)
  hydrogen bonds       : angle       3.82352 ( 1962)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 31
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9665 (tmm) cc_final: 0.9374 (tmm)
REVERT: A  159 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9469 (tt)
REVERT: A  280 MET cc_start: 0.9379 (ttp) cc_final: 0.8986 (tpp)
REVERT: A  320 MET cc_start: 0.9610 (ptp) cc_final: 0.9347 (pmm)
REVERT: A  335 MET cc_start: 0.9322 (mpp) cc_final: 0.8894 (mtm)
REVERT: A  433 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9439 (pp)
REVERT: A  592 MET cc_start: 0.9339 (mtp) cc_final: 0.9029 (mtp)
REVERT: B   67 MET cc_start: 0.9576 (tpp) cc_final: 0.9369 (tpp)
REVERT: B  154 MET cc_start: 0.9689 (tmm) cc_final: 0.9415 (tmm)
REVERT: B  159 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9408 (tt)
REVERT: B  433 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9456 (pp)
REVERT: B  592 MET cc_start: 0.9430 (mtp) cc_final: 0.9124 (mtp)
  outliers start: 19
  outliers final: 14
  residues processed: 48
  average time/residue: 0.0681
  time to fit residues: 5.5533
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 31
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  433 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
B 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.034722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.026209 restraints weight = 83765.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.027065 restraints weight = 51546.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.027672 restraints weight = 37366.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.028107 restraints weight = 29877.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.028396 restraints weight = 25519.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9326  Z= 0.128
  Angle     :  0.586  11.983  12668  Z= 0.299
  Chirality :  0.040   0.200   1484
  Planarity :  0.003   0.032   1616
  Dihedral  :  3.583  22.342   1306
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.19 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.24), residues: 1174
  helix:  2.30 (0.18), residues: 800
  sheet: -0.89 (0.62), residues: 72
  loop :  0.16 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 531 
 TYR   0.009   0.001   TYR A 195 
 PHE   0.014   0.001   PHE B 121 
 TRP   0.008   0.001   TRP B 291 
 HIS   0.002   0.000   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9326)
  covalent geometry    : angle       0.58638 (12668)
  hydrogen bonds       : bond        0.04471 (  668)
  hydrogen bonds       : angle       3.81465 ( 1962)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1513.81 seconds
wall clock time: 26 minutes 55.70 seconds (1615.70 seconds total)