Starting phenix.real_space_refine
on Thu Jul  2 22:24:37 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2026/7r8a_24313.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6810      2.51       5
     N    1778      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10530
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4596
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 22, 'TRANS': 561}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4202
          Classifications: {'peptide': 529}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 901
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 803
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.47, per 1000 atoms: 0.23
  Number of scatterers: 10530
  At special positions: 0
  Unit cell: (117.316, 99.592, 128.288, 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      66     16.00
     O    1876      8.00
     N    1778      7.00
     C    6810      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 587 " - pdb=" SG  CYS A 600 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 296.7 milliseconds
  

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2468

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      51.5% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 4.597A  pdb=" N   PHE A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 175 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 253 through 257
      removed outlier: 3.576A  pdb=" N   LEU A 256 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 288
      removed outlier: 3.810A  pdb=" N   GLY A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 313 through 331
    Processing helix  chain 'A' and resid 332 through 347
      removed outlier: 3.917A  pdb=" N   HIS A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   HIS A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 381
    Processing helix  chain 'A' and resid 382 through 404
      removed outlier: 3.613A  pdb=" N   VAL A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ASN A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   LEU A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE A 403 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 453
      Proline residue:  A 431  - end of helix
      Proline residue:  A 443  - end of helix
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 459 through 491
      removed outlier: 3.585A  pdb=" N   MET A 463 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
      Proline residue:  A 473  - end of helix
      removed outlier: 4.839A  pdb=" N   TRP A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 524
      Proline residue:  A 509  - end of helix
    Processing helix  chain 'A' and resid 526 through 545
    Processing helix  chain 'A' and resid 556 through 564
      removed outlier: 3.608A  pdb=" N   TYR A 564 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 580
      removed outlier: 4.329A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
      removed outlier: 3.641A  pdb=" N   PHE A 608 " --> pdb=" O   GLN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 629
    Processing helix  chain 'A' and resid 630 through 646
      removed outlier: 3.974A  pdb=" N   LEU A 634 " --> pdb=" O   PHE A 630 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A 635 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 120
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 162 through 175
    Processing helix  chain 'B' and resid 180 through 195
    Processing helix  chain 'B' and resid 214 through 227
    Processing helix  chain 'B' and resid 244 through 260
    Processing helix  chain 'B' and resid 299 through 305
    Processing helix  chain 'B' and resid 316 through 325
      removed outlier: 3.773A  pdb=" N   THR B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 411
    Processing helix  chain 'B' and resid 413 through 435
    Processing helix  chain 'B' and resid 444 through 473
      removed outlier: 4.644A  pdb=" N   ILE B 459 " --> pdb=" O   ILE B 455 " (cutoff:3.500A)
      Proline residue:  B 460  - end of helix
    Processing helix  chain 'B' and resid 474 through 484
    Processing helix  chain 'B' and resid 490 through 517
      removed outlier: 4.210A  pdb=" N   PHE B 494 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      Proline residue:  B 502  - end of helix
      Proline residue:  B 514  - end of helix
      removed outlier: 4.259A  pdb=" N   TRP B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 553
    Processing helix  chain 'B' and resid 555 through 573
    Processing helix  chain 'B' and resid 585 through 593
    Processing helix  chain 'B' and resid 594 through 609
    Processing helix  chain 'B' and resid 627 through 633
      removed outlier: 3.617A  pdb=" N   MET B 633 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 665
    Processing helix  chain 'C' and resid 72 through 76
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 4.009A  pdb=" N   LEU D 103 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77
      removed outlier: 6.724A  pdb=" N   LYS A  70 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   SER A  44 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   VAL A  72 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A  43 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LEU A 110 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL A 113 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132
      removed outlier: 3.923A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   SER A 267 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU A 271 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96
      removed outlier: 7.513A  pdb=" N   PHE B  93 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ARG B  50 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   VAL B  95 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   GLU B  48 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.373A  pdb=" N   ALA B 149 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ASP B 237 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL B 151 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU B 101 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   MET B 100 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU B 284 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ALA B 102 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   MET B 286 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ILE B 104 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU B 294 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU B 285 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26
    Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81
      removed outlier: 4.974A  pdb=" N   TRP C  66 " --> pdb=" O   ARG C  57 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ARG C  57 " --> pdb=" O   TRP C  66 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27
    Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32
      removed outlier: 5.852A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE D  68 " --> pdb=" O   TRP D  55 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   GLN D  57 " --> pdb=" O   ARG D  66 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   ARG D  66 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32
      removed outlier: 5.852A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR D 117 " --> pdb=" O   GLN D 110 " (cutoff:3.500A)

    578 hydrogen bonds defined for protein.
    1674 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: 1.96

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3340
        1.35 -     1.47: 2622
        1.47 -     1.59: 4693
        1.59 -     1.71: 0
        1.71 -     1.83: 105
  Bond restraints: 10760
  Sorted by residual:
  bond pdb=" C10 CLR A 701 "
       pdb=" C5  CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.519  1.450  0.069 2.00e-02 2.50e+03 1.18e+01
  bond pdb=" C10 CLR A 701 "
       pdb=" C19 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.536  1.485  0.051 2.00e-02 2.50e+03 6.61e+00
  bond pdb=" C1  CLR A 701 "
       pdb=" C10 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.544  1.498  0.046 2.00e-02 2.50e+03 5.31e+00
  bond pdb=" C13 CLR A 701 "
       pdb=" C18 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.486  0.046 2.00e-02 2.50e+03 5.30e+00
  bond pdb=" C16 CLR A 701 "
       pdb=" C17 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.554  1.511  0.043 2.00e-02 2.50e+03 4.57e+00
  ... (remaining 10755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 14383
        2.02 -     4.04: 146
        4.04 -     6.06: 28
        6.06 -     8.08: 9
        8.08 -    10.10: 3
  Bond angle restraints: 14569
  Sorted by residual:
  angle pdb=" N   GLN A 310 "
        pdb=" CA  GLN A 310 "
        pdb=" C   GLN A 310 "
      ideal   model   delta    sigma   weight residual
     114.56  108.87    5.69 1.27e+00 6.20e-01 2.01e+01
  angle pdb=" C   LEU B 458 "
        pdb=" N   ILE B 459 "
        pdb=" CA  ILE B 459 "
      ideal   model   delta    sigma   weight residual
     120.24  122.77   -2.53 6.30e-01 2.52e+00 1.62e+01
  angle pdb=" C   ILE B 459 "
        pdb=" CA  ILE B 459 "
        pdb=" CB  ILE B 459 "
      ideal   model   delta    sigma   weight residual
     114.35  110.19    4.16 1.06e+00 8.90e-01 1.54e+01
  angle pdb=" C   THR B 488 "
        pdb=" N   THR B 489 "
        pdb=" CA  THR B 489 "
      ideal   model   delta    sigma   weight residual
     121.54  128.02   -6.48 1.91e+00 2.74e-01 1.15e+01
  angle pdb=" C16 CLR A 701 "
        pdb=" C17 CLR A 701 "
        pdb=" C20 CLR A 701 "
      ideal   model   delta    sigma   weight residual
     112.02  101.92   10.10 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 14564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5807
       17.52 -    35.04: 449
       35.04 -    52.55: 107
       52.55 -    70.07: 24
       70.07 -    87.59: 7
  Dihedral angle restraints: 6394
    sinusoidal: 2550
      harmonic: 3844
  Sorted by residual:
  dihedral pdb=" CA  THR A 358 "
           pdb=" C   THR A 358 "
           pdb=" N   LYS A 359 "
           pdb=" CA  LYS A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.63  -16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ILE C 114 "
           pdb=" C   ILE C 114 "
           pdb=" N   TYR C 115 "
           pdb=" CA  TYR C 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.91  -16.09     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CB  GLU A 579 "
           pdb=" CG  GLU A 579 "
           pdb=" CD  GLU A 579 "
           pdb=" OE1 GLU A 579 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.59   87.59     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 6391 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1583
       0.089 -    0.178: 75
       0.178 -    0.267: 2
       0.267 -    0.356: 0
       0.356 -    0.445: 2
  Chirality restraints: 1662
  Sorted by residual:
  chirality pdb=" C13 CLR A 701 "
            pdb=" C12 CLR A 701 "
            pdb=" C14 CLR A 701 "
            pdb=" C17 CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.49   -0.45 2.00e-01 2.50e+01 4.95e+00
  chirality pdb=" C10 CLR A 701 "
            pdb=" C1  CLR A 701 "
            pdb=" C5  CLR A 701 "
            pdb=" C9  CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.45   -0.39 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" C17 CLR A 701 "
            pdb=" C13 CLR A 701 "
            pdb=" C16 CLR A 701 "
            pdb=" C20 CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.81   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1659 not shown)

  Planarity restraints: 1827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 490 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO B 491 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 491 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 491 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 276 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO A 277 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  78 "    0.020 5.00e-02 4.00e+02   3.07e-02 1.51e+00
        pdb=" N   PRO D  79 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO D  79 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  79 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1824 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3300
        2.82 -     3.34: 9420
        3.34 -     3.86: 17278
        3.86 -     4.38: 19310
        4.38 -     4.90: 34751
  Nonbonded interactions: 84059
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 550 "
            pdb=" O   LEU B 434 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" ND2 ASN A 296 "
            pdb=" OD2 ASP A 299 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   SER A  46 "
            pdb=" OG  SER A  46 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   GLU A 315 "
            pdb=" OG  SER A 319 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ALA A 601 "
            pdb=" NE2 GLN A 607 "
     model   vdw
     2.315 3.120
  ... (remaining 84054 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             2.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.540
  Find NCS groups from input model:        0.060
  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:11.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
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      :  0.003   0.069  10763  Z= 0.137
  Angle     :  0.571  10.099  14575  Z= 0.313
  Chirality :  0.041   0.445   1662
  Planarity :  0.003   0.039   1827
  Dihedral  : 13.746  87.589   3917
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.59 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.58 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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 (0.21), residues: 1308
  helix: -0.04 (0.19), residues: 675
  sheet: -0.90 (0.33), residues: 185
  loop : -2.75 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 121 
 TYR   0.009   0.001   TYR B 507 
 PHE   0.007   0.001   PHE B 493 
 TRP   0.008   0.001   TRP B 584 
 HIS   0.003   0.000   HIS A 470 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.14 (10760)
  covalent geometry    : angle       0.57105 /  0.31 (14569)
  SS BOND              : bond        0.00220 /  0.14 (    3)
  SS BOND              : angle       0.66554 /  0.43 (    6)
  hydrogen bonds       : bond        0.12589 /  8.05 (  574)
  hydrogen bonds       : angle       4.94407 /  3.53 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 229
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7154 (pt0)
REVERT: A  114 TYR cc_start: 0.8290 (m-80) cc_final: 0.6925 (m-80)
REVERT: A  118 ARG cc_start: 0.7274 (mpt180) cc_final: 0.6894 (mmt90)
REVERT: A  169 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7437 (mm-30)
REVERT: A  224 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7354 (p0)
REVERT: A  302 MET cc_start: 0.7524 (mmm) cc_final: 0.7225 (tpp)
REVERT: A  387 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7358 (mp)
REVERT: B   89 GLN cc_start: 0.8371 (mt0) cc_final: 0.7729 (mp10)
REVERT: B   94 LYS cc_start: 0.8581 (tttm) cc_final: 0.8360 (tptm)
REVERT: B  267 ILE cc_start: 0.8736 (mt) cc_final: 0.8458 (pt)
REVERT: B  281 ASP cc_start: 0.8360 (t0) cc_final: 0.8032 (t0)
REVERT: B  309 TYR cc_start: 0.8340 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  404 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7232 (mtm110)
REVERT: B  459 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (tp)
REVERT: B  517 TRP cc_start: 0.6979 (m100) cc_final: 0.6372 (t60)
REVERT: C   80 ASP cc_start: 0.8443 (t0) cc_final: 0.8135 (t0)
REVERT: C   99 ILE cc_start: 0.8604 (mt) cc_final: 0.8313 (mp)
REVERT: C  130 GLN cc_start: 0.8066 (mp-120) cc_final: 0.7774 (pp30)
REVERT: D   78 VAL cc_start: 0.8061 (p) cc_final: 0.7752 (t)
REVERT: D  101 GLU cc_start: 0.6566 (mp0) cc_final: 0.6044 (mp0)
  outliers start: 39
  outliers final: 3
  residues processed: 259
  average time/residue: 0.5411
  time to fit residues: 150.9573
Evaluate side-chains
  147 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain B residue  275 ASP
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  459 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.5164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 116 ASN
A 160 ASN
A 206 GLN
A 392 GLN
A 437 ASN
A 459 GLN
A 462 GLN
A 510 HIS
A 578 ASN
A 604 GLN
A 607 GLN
B  99 GLN
B 131 GLN
B 150 HIS
B 199 GLN
B 249 HIS
B 409 ASN
B 438 HIS
B 462 ASN
C  58 GLN
C  75 ASN
C 105 ASN
C 130 GLN
D  26 GLN
D  47 GLN
D  57 GLN
D  58 GLN
D  65 GLN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.109414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.082233 restraints weight = 14861.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 2.08
r_work: 0.2738 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9109
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10763  Z= 0.183
  Angle     :  0.645   6.957  14575  Z= 0.331
  Chirality :  0.044   0.144   1662
  Planarity :  0.005   0.057   1827
  Dihedral  :  5.043  56.322   1477
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 20.05 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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: -0.33 (0.23), residues: 1308
  helix:  1.03 (0.20), residues: 682
  sheet: -0.35 (0.36), residues: 177
  loop : -2.13 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 313 
 TYR   0.017   0.002   TYR A 628 
 PHE   0.021   0.002   PHE A 642 
 TRP   0.017   0.002   TRP B 584 
 HIS   0.010   0.001   HIS A 510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.18 (10760)
  covalent geometry    : angle       0.64474 /  0.33 (14569)
  SS BOND              : bond        0.00671 /  0.44 (    3)
  SS BOND              : angle       1.21948 /  0.77 (    6)
  hydrogen bonds       : bond        0.05847 /  3.80 (  574)
  hydrogen bonds       : angle       3.97444 /  2.79 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 147
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7908 (mpt180) cc_final: 0.7247 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8240 (mm-30)
REVERT: A  343 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8057 (tm-30)
REVERT: A  353 MET cc_start: 0.6278 (pmm) cc_final: 0.5795 (pmm)
REVERT: A  383 LYS cc_start: 0.7637 (mppt) cc_final: 0.7218 (mmtm)
REVERT: A  387 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: A  454 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7804 (mm-40)
REVERT: A  536 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8574 (tp)
REVERT: B   26 ARG cc_start: 0.6370 (pmt170) cc_final: 0.6154 (ppt-90)
REVERT: B   89 GLN cc_start: 0.8810 (mt0) cc_final: 0.8285 (mt0)
REVERT: B  404 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8364 (mtm110)
REVERT: B  505 CYS cc_start: 0.9244 (t) cc_final: 0.8875 (m)
REVERT: B  517 TRP cc_start: 0.7896 (m100) cc_final: 0.7502 (t60)
REVERT: B  582 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6859 (p)
REVERT: C   80 ASP cc_start: 0.8913 (t0) cc_final: 0.8680 (t0)
REVERT: C   99 ILE cc_start: 0.8888 (mt) cc_final: 0.8576 (mp)
REVERT: C  103 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7890 (mm110)
REVERT: C  130 GLN cc_start: 0.8475 (mp10) cc_final: 0.8247 (pm20)
REVERT: D   37 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7668 (pm20)
REVERT: D  103 LEU cc_start: 0.8516 (tp) cc_final: 0.8314 (tt)
  outliers start: 52
  outliers final: 20
  residues processed: 186
  average time/residue: 0.5508
  time to fit residues: 109.9412
Evaluate side-chains
  155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   37 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 126 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 122 optimal weight:    8.9990
   chunk 129 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
A 493 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.080953 restraints weight = 14791.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 2.05
r_work: 0.2728 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2593 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9190
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10763  Z= 0.166
  Angle     :  0.597   6.818  14575  Z= 0.306
  Chirality :  0.043   0.172   1662
  Planarity :  0.004   0.053   1827
  Dihedral  :  4.780  52.500   1472
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 20.31 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.17 (0.23), residues: 1308
  helix:  1.39 (0.20), residues: 677
  sheet: -0.22 (0.36), residues: 188
  loop : -1.77 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 550 
 TYR   0.014   0.001   TYR A 581 
 PHE   0.016   0.002   PHE B 493 
 TRP   0.018   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.17 (10760)
  covalent geometry    : angle       0.59655 /  0.31 (14569)
  SS BOND              : bond        0.00632 /  0.42 (    3)
  SS BOND              : angle       0.92722 /  0.53 (    6)
  hydrogen bonds       : bond        0.05546 /  3.61 (  574)
  hydrogen bonds       : angle       3.90063 /  2.74 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 142
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8075 (mpt180) cc_final: 0.7429 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8324 (mm-30)
REVERT: A  343 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8213 (tm-30)
REVERT: A  353 MET cc_start: 0.6467 (pmm) cc_final: 0.6015 (pmm)
REVERT: A  383 LYS cc_start: 0.7730 (mppt) cc_final: 0.7460 (mmtm)
REVERT: A  454 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7933 (mm-40)
REVERT: A  536 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8687 (tp)
REVERT: B   89 GLN cc_start: 0.8866 (mt0) cc_final: 0.8457 (mt0)
REVERT: B  142 GLN cc_start: 0.8392 (pp30) cc_final: 0.8131 (tm-30)
REVERT: B  404 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8465 (mtm110)
REVERT: B  427 MET cc_start: 0.8663 (tpp) cc_final: 0.8463 (mmp)
REVERT: B  505 CYS cc_start: 0.9238 (t) cc_final: 0.8913 (m)
REVERT: B  517 TRP cc_start: 0.7958 (m100) cc_final: 0.7681 (t60)
REVERT: C   38 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7830 (mtp180)
REVERT: C   80 ASP cc_start: 0.8970 (t0) cc_final: 0.8755 (t0)
REVERT: C   99 ILE cc_start: 0.8977 (mt) cc_final: 0.8676 (mp)
REVERT: D   44 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8235 (ttt90)
  outliers start: 50
  outliers final: 20
  residues processed: 181
  average time/residue: 0.5413
  time to fit residues: 105.1259
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  483 SER
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 120 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.108096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.080816 restraints weight = 15004.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.12
r_work: 0.2719 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2585 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9092
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10763  Z= 0.118
  Angle     :  0.546   6.732  14575  Z= 0.278
  Chirality :  0.040   0.149   1662
  Planarity :  0.004   0.061   1827
  Dihedral  :  4.339  54.815   1467
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.92 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.59 (0.24), residues: 1308
  helix:  1.74 (0.20), residues: 679
  sheet: -0.08 (0.35), residues: 194
  loop : -1.60 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 313 
 TYR   0.011   0.001   TYR A 487 
 PHE   0.013   0.001   PHE B 493 
 TRP   0.017   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (10760)
  covalent geometry    : angle       0.54477 /  0.28 (14569)
  SS BOND              : bond        0.00448 /  0.29 (    3)
  SS BOND              : angle       1.77592 /  1.36 (    6)
  hydrogen bonds       : bond        0.04560 /  2.96 (  574)
  hydrogen bonds       : angle       3.78043 /  2.67 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7378 (tt0)
REVERT: A  118 ARG cc_start: 0.7857 (mpt180) cc_final: 0.7459 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8263 (mm-30)
REVERT: A  324 MET cc_start: 0.8433 (tmm) cc_final: 0.8065 (tmt)
REVERT: A  343 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8154 (tm-30)
REVERT: A  353 MET cc_start: 0.6355 (pmm) cc_final: 0.6135 (pmm)
REVERT: A  383 LYS cc_start: 0.7536 (mppt) cc_final: 0.7109 (mmtm)
REVERT: A  387 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: A  400 LEU cc_start: 0.8865 (tp) cc_final: 0.8549 (mt)
REVERT: A  454 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7884 (mm-40)
REVERT: A  536 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8531 (tp)
REVERT: B   89 GLN cc_start: 0.8891 (mt0) cc_final: 0.8440 (mt0)
REVERT: B  142 GLN cc_start: 0.8267 (pp30) cc_final: 0.7860 (tm-30)
REVERT: B  404 ARG cc_start: 0.8729 (mtp-110) cc_final: 0.8335 (mtm110)
REVERT: B  427 MET cc_start: 0.8558 (tpp) cc_final: 0.8353 (mmp)
REVERT: B  505 CYS cc_start: 0.9139 (t) cc_final: 0.8681 (m)
REVERT: B  517 TRP cc_start: 0.7916 (m100) cc_final: 0.7471 (t60)
REVERT: C   80 ASP cc_start: 0.8913 (t0) cc_final: 0.8619 (t0)
REVERT: C   99 ILE cc_start: 0.8824 (mt) cc_final: 0.8487 (mp)
REVERT: C  103 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7696 (mm110)
REVERT: D   44 ARG cc_start: 0.8465 (ttt90) cc_final: 0.8247 (ttt90)
  outliers start: 35
  outliers final: 14
  residues processed: 165
  average time/residue: 0.5516
  time to fit residues: 97.9798
Evaluate side-chains
  146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   95 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
A 393 ASN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.104211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.077079 restraints weight = 14863.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 2.07
r_work: 0.2637 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2501 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9148
moved from start:          0.4347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10763  Z= 0.174
  Angle     :  0.610   8.113  14575  Z= 0.313
  Chirality :  0.043   0.187   1662
  Planarity :  0.004   0.054   1827
  Dihedral  :  4.558  51.918   1467
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.20 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.97 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.59 (0.24), residues: 1308
  helix:  1.64 (0.20), residues: 681
  sheet:  0.03 (0.36), residues: 194
  loop : -1.46 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 550 
 TYR   0.014   0.002   TYR A 581 
 PHE   0.019   0.002   PHE B 493 
 TRP   0.019   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.17 (10760)
  covalent geometry    : angle       0.60855 /  0.31 (14569)
  SS BOND              : bond        0.00655 /  0.45 (    3)
  SS BOND              : angle       1.94160 /  1.44 (    6)
  hydrogen bonds       : bond        0.05751 /  3.75 (  574)
  hydrogen bonds       : angle       3.92863 /  2.77 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7470 (tt0)
REVERT: A  118 ARG cc_start: 0.7931 (mpt180) cc_final: 0.7509 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8301 (mm-30)
REVERT: A  324 MET cc_start: 0.8413 (tmm) cc_final: 0.8147 (tmm)
REVERT: A  343 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8184 (tm-30)
REVERT: A  383 LYS cc_start: 0.7705 (mppt) cc_final: 0.7261 (mmtm)
REVERT: A  387 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8266 (mp)
REVERT: A  454 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7828 (mm-40)
REVERT: A  536 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8524 (tp)
REVERT: B   89 GLN cc_start: 0.8880 (mt0) cc_final: 0.8441 (mt0)
REVERT: B   94 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8688 (tttm)
REVERT: B  142 GLN cc_start: 0.8240 (pp30) cc_final: 0.7864 (tm-30)
REVERT: B  404 ARG cc_start: 0.8739 (mtp-110) cc_final: 0.8342 (mtm110)
REVERT: B  427 MET cc_start: 0.8642 (tpp) cc_final: 0.8428 (mmp)
REVERT: B  505 CYS cc_start: 0.9196 (t) cc_final: 0.8806 (m)
REVERT: B  517 TRP cc_start: 0.7887 (m100) cc_final: 0.7478 (t60)
REVERT: C   80 ASP cc_start: 0.8904 (t0) cc_final: 0.8605 (t0)
REVERT: C  103 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7766 (mm110)
REVERT: C  130 GLN cc_start: 0.8043 (pp30) cc_final: 0.7843 (pp30)
  outliers start: 42
  outliers final: 24
  residues processed: 169
  average time/residue: 0.5704
  time to fit residues: 103.5574
Evaluate side-chains
  152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 129 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 72 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.105155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.078091 restraints weight = 14912.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 2.08
r_work: 0.2661 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9133
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10763  Z= 0.146
  Angle     :  0.582   8.245  14575  Z= 0.297
  Chirality :  0.041   0.172   1662
  Planarity :  0.004   0.055   1827
  Dihedral  :  4.492  51.988   1467
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.97 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.72 (0.24), residues: 1308
  helix:  1.80 (0.20), residues: 674
  sheet:  0.21 (0.37), residues: 184
  loop : -1.50 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 550 
 TYR   0.012   0.001   TYR A 487 
 PHE   0.016   0.001   PHE B 493 
 TRP   0.017   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 (10760)
  covalent geometry    : angle       0.58130 /  0.30 (14569)
  SS BOND              : bond        0.00573 /  0.39 (    3)
  SS BOND              : angle       1.52846 /  1.08 (    6)
  hydrogen bonds       : bond        0.05215 /  3.39 (  574)
  hydrogen bonds       : angle       3.88011 /  2.74 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 130
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7468 (tt0)
REVERT: A  118 ARG cc_start: 0.7868 (mpt180) cc_final: 0.7438 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8329 (mm-30)
REVERT: A  324 MET cc_start: 0.8386 (tmm) cc_final: 0.8103 (tmm)
REVERT: A  343 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8181 (tm-30)
REVERT: A  383 LYS cc_start: 0.7666 (mppt) cc_final: 0.7230 (mmtm)
REVERT: A  387 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8236 (mp)
REVERT: A  454 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7880 (mm-40)
REVERT: A  536 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8513 (tp)
REVERT: B   26 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5865 (ppt-90)
REVERT: B   89 GLN cc_start: 0.8898 (mt0) cc_final: 0.8481 (mt0)
REVERT: B   94 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8646 (tttm)
REVERT: B  142 GLN cc_start: 0.8230 (pp30) cc_final: 0.7857 (tm-30)
REVERT: B  404 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8330 (mtm110)
REVERT: B  427 MET cc_start: 0.8618 (tpp) cc_final: 0.8401 (mmp)
REVERT: B  429 MET cc_start: 0.8536 (ptm) cc_final: 0.7796 (mmt)
REVERT: B  505 CYS cc_start: 0.9193 (t) cc_final: 0.8774 (m)
REVERT: B  517 TRP cc_start: 0.7887 (m100) cc_final: 0.7451 (t60)
REVERT: C   80 ASP cc_start: 0.8907 (t0) cc_final: 0.8619 (t0)
REVERT: C  103 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7711 (mm110)
  outliers start: 44
  outliers final: 23
  residues processed: 164
  average time/residue: 0.5432
  time to fit residues: 95.7891
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 120 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 127 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 123 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.106179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.079046 restraints weight = 14871.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 2.10
r_work: 0.2686 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2551 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9134
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10763  Z= 0.128
  Angle     :  0.557   7.667  14575  Z= 0.285
  Chirality :  0.041   0.168   1662
  Planarity :  0.004   0.055   1827
  Dihedral  :  4.380  52.422   1467
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 19.88 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.86 (0.24), residues: 1308
  helix:  1.90 (0.20), residues: 674
  sheet:  0.30 (0.36), residues: 192
  loop : -1.46 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 550 
 TYR   0.011   0.001   TYR A 487 
 PHE   0.015   0.001   PHE C  89 
 TRP   0.011   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (10760)
  covalent geometry    : angle       0.55680 /  0.29 (14569)
  SS BOND              : bond        0.00554 /  0.37 (    3)
  SS BOND              : angle       1.32864 /  0.92 (    6)
  hydrogen bonds       : bond        0.04776 /  3.10 (  574)
  hydrogen bonds       : angle       3.80303 /  2.69 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 139
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7920 (mpt180) cc_final: 0.7489 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8373 (mm-30)
REVERT: A  324 MET cc_start: 0.8404 (tmm) cc_final: 0.8129 (tmm)
REVERT: A  343 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8169 (tm-30)
REVERT: A  383 LYS cc_start: 0.7642 (mppt) cc_final: 0.7229 (mmtm)
REVERT: A  387 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8270 (mp)
REVERT: A  454 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7870 (mm-40)
REVERT: A  536 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8530 (tp)
REVERT: B   26 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5853 (ppt-90)
REVERT: B   89 GLN cc_start: 0.8900 (mt0) cc_final: 0.8447 (mt0)
REVERT: B   94 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8619 (tttm)
REVERT: B  142 GLN cc_start: 0.8237 (pp30) cc_final: 0.7875 (tm-30)
REVERT: B  404 ARG cc_start: 0.8755 (mtp-110) cc_final: 0.8334 (mtm110)
REVERT: B  427 MET cc_start: 0.8634 (tpp) cc_final: 0.8417 (mmp)
REVERT: B  429 MET cc_start: 0.8535 (ptm) cc_final: 0.7857 (mmt)
REVERT: B  505 CYS cc_start: 0.9198 (t) cc_final: 0.8766 (m)
REVERT: B  517 TRP cc_start: 0.7919 (m100) cc_final: 0.7511 (t60)
REVERT: C   80 ASP cc_start: 0.8895 (t0) cc_final: 0.8607 (t0)
REVERT: C   99 ILE cc_start: 0.8792 (mt) cc_final: 0.8466 (mp)
REVERT: C  103 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7675 (mm110)
  outliers start: 43
  outliers final: 26
  residues processed: 170
  average time/residue: 0.6150
  time to fit residues: 112.0080
Evaluate side-chains
  163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 91 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.105930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.078810 restraints weight = 14788.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 2.09
r_work: 0.2674 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9134
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10763  Z= 0.136
  Angle     :  0.576   8.511  14575  Z= 0.294
  Chirality :  0.041   0.157   1662
  Planarity :  0.004   0.062   1827
  Dihedral  :  4.402  52.322   1467
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 20.40 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.90 (0.24), residues: 1308
  helix:  1.84 (0.20), residues: 685
  sheet:  0.42 (0.37), residues: 184
  loop : -1.37 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 550 
 TYR   0.011   0.001   TYR A 487 
 PHE   0.015   0.001   PHE B 493 
 TRP   0.011   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 (10760)
  covalent geometry    : angle       0.57503 /  0.29 (14569)
  SS BOND              : bond        0.00561 /  0.37 (    3)
  SS BOND              : angle       1.41865 /  0.95 (    6)
  hydrogen bonds       : bond        0.04906 /  3.19 (  574)
  hydrogen bonds       : angle       3.82034 /  2.70 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 131
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7967 (tt0) cc_final: 0.7673 (tt0)
REVERT: A  118 ARG cc_start: 0.7982 (mpt180) cc_final: 0.7373 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8388 (mm-30)
REVERT: A  324 MET cc_start: 0.8398 (tmm) cc_final: 0.8119 (tmm)
REVERT: A  343 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8164 (tm-30)
REVERT: A  383 LYS cc_start: 0.7656 (mppt) cc_final: 0.7243 (mmtm)
REVERT: A  387 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8265 (mp)
REVERT: A  454 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.7867 (mm-40)
REVERT: A  536 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8524 (tp)
REVERT: B   26 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5819 (ppt-90)
REVERT: B   89 GLN cc_start: 0.8890 (mt0) cc_final: 0.8431 (mt0)
REVERT: B  142 GLN cc_start: 0.8219 (pp30) cc_final: 0.7865 (tm-30)
REVERT: B  404 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8339 (mtm110)
REVERT: B  427 MET cc_start: 0.8634 (tpp) cc_final: 0.8417 (mmp)
REVERT: B  429 MET cc_start: 0.8508 (ptm) cc_final: 0.7856 (mmt)
REVERT: B  505 CYS cc_start: 0.9190 (t) cc_final: 0.8762 (m)
REVERT: B  517 TRP cc_start: 0.7896 (m100) cc_final: 0.7462 (t60)
REVERT: C   38 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7760 (mtp180)
REVERT: C   80 ASP cc_start: 0.8896 (t0) cc_final: 0.8610 (t0)
REVERT: C   99 ILE cc_start: 0.8810 (mt) cc_final: 0.8488 (mp)
REVERT: C  103 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7479 (tp40)
REVERT: D   44 ARG cc_start: 0.8384 (ttt90) cc_final: 0.7992 (ttt90)
  outliers start: 41
  outliers final: 25
  residues processed: 163
  average time/residue: 0.5642
  time to fit residues: 98.7777
Evaluate side-chains
  160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.076890 restraints weight = 14843.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.08
r_work: 0.2646 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9162
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10763  Z= 0.168
  Angle     :  0.615  11.366  14575  Z= 0.314
  Chirality :  0.042   0.159   1662
  Planarity :  0.004   0.058   1827
  Dihedral  :  4.517  50.485   1467
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.43 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 20.57 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.84 (0.24), residues: 1308
  helix:  1.81 (0.20), residues: 679
  sheet:  0.29 (0.36), residues: 194
  loop : -1.36 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 550 
 TYR   0.012   0.001   TYR A 487 
 PHE   0.018   0.001   PHE B 493 
 TRP   0.012   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.17 (10760)
  covalent geometry    : angle       0.61385 /  0.31 (14569)
  SS BOND              : bond        0.00608 /  0.41 (    3)
  SS BOND              : angle       1.54448 /  1.03 (    6)
  hydrogen bonds       : bond        0.05506 /  3.59 (  574)
  hydrogen bonds       : angle       3.89898 /  2.75 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.8014 (tt0) cc_final: 0.7708 (tt0)
REVERT: A  118 ARG cc_start: 0.8017 (mpt180) cc_final: 0.7642 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8417 (mm-30)
REVERT: A  324 MET cc_start: 0.8411 (tmm) cc_final: 0.8123 (tmm)
REVERT: A  343 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8185 (tm-30)
REVERT: A  383 LYS cc_start: 0.7748 (mppt) cc_final: 0.7317 (mmtm)
REVERT: A  387 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8301 (mp)
REVERT: A  454 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7859 (mm-40)
REVERT: A  536 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8519 (tp)
REVERT: B   26 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5853 (ppt-90)
REVERT: B   89 GLN cc_start: 0.8877 (mt0) cc_final: 0.8460 (mt0)
REVERT: B  121 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6881 (mpt180)
REVERT: B  142 GLN cc_start: 0.8230 (pp30) cc_final: 0.7898 (tm-30)
REVERT: B  404 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.8338 (mtm110)
REVERT: B  427 MET cc_start: 0.8679 (tpp) cc_final: 0.8458 (mmp)
REVERT: B  429 MET cc_start: 0.8526 (ptm) cc_final: 0.7917 (mmt)
REVERT: B  505 CYS cc_start: 0.9219 (t) cc_final: 0.8838 (m)
REVERT: B  517 TRP cc_start: 0.7912 (m100) cc_final: 0.7510 (t60)
REVERT: C   38 ARG cc_start: 0.8058 (ttp-170) cc_final: 0.7749 (mtp180)
REVERT: C   80 ASP cc_start: 0.8898 (t0) cc_final: 0.8629 (t0)
REVERT: C   99 ILE cc_start: 0.8796 (mt) cc_final: 0.8476 (mp)
REVERT: C  103 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7435 (tp40)
REVERT: D   44 ARG cc_start: 0.8419 (ttt90) cc_final: 0.8216 (ttt180)
  outliers start: 39
  outliers final: 28
  residues processed: 161
  average time/residue: 0.5725
  time to fit residues: 98.9987
Evaluate side-chains
  163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0570
   chunk 114 optimal weight:    0.9990
   chunk 123 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9504

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.105525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.078494 restraints weight = 14706.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 2.07
r_work: 0.2681 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2548 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9135
moved from start:          0.4495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10763  Z= 0.132
  Angle     :  0.593  12.459  14575  Z= 0.299
  Chirality :  0.041   0.158   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.417  50.984   1467
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.01 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  1.02 (0.24), residues: 1308
  helix:  1.97 (0.20), residues: 679
  sheet:  0.37 (0.36), residues: 194
  loop : -1.30 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 313 
 TYR   0.012   0.001   TYR A 487 
 PHE   0.015   0.001   PHE B 493 
 TRP   0.010   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 (10760)
  covalent geometry    : angle       0.59235 /  0.30 (14569)
  SS BOND              : bond        0.00531 /  0.35 (    3)
  SS BOND              : angle       1.32719 /  0.89 (    6)
  hydrogen bonds       : bond        0.04868 /  3.16 (  574)
  hydrogen bonds       : angle       3.83675 /  2.71 ( 1674)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.8011 (tt0) cc_final: 0.7701 (tt0)
REVERT: A  118 ARG cc_start: 0.8005 (mpt180) cc_final: 0.7627 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8425 (mm-30)
REVERT: A  324 MET cc_start: 0.8401 (tmm) cc_final: 0.8106 (tmm)
REVERT: A  343 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8162 (tm-30)
REVERT: A  383 LYS cc_start: 0.7679 (mppt) cc_final: 0.7272 (mmtm)
REVERT: A  387 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: A  454 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7877 (mm-40)
REVERT: A  536 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8522 (tp)
REVERT: B   26 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5843 (ppt-90)
REVERT: B   89 GLN cc_start: 0.8888 (mt0) cc_final: 0.8434 (mt0)
REVERT: B  121 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6824 (mpt180)
REVERT: B  142 GLN cc_start: 0.8213 (pp30) cc_final: 0.7877 (tm-30)
REVERT: B  404 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8327 (mtm110)
REVERT: B  427 MET cc_start: 0.8664 (tpp) cc_final: 0.8462 (mmp)
REVERT: B  429 MET cc_start: 0.8454 (ptm) cc_final: 0.7849 (mmt)
REVERT: B  505 CYS cc_start: 0.9191 (t) cc_final: 0.8773 (m)
REVERT: B  517 TRP cc_start: 0.7889 (m100) cc_final: 0.7459 (t60)
REVERT: C   80 ASP cc_start: 0.8897 (t0) cc_final: 0.8615 (t0)
REVERT: C   99 ILE cc_start: 0.8788 (mt) cc_final: 0.8469 (mp)
REVERT: D   44 ARG cc_start: 0.8410 (ttt90) cc_final: 0.8147 (ttt90)
  outliers start: 34
  outliers final: 25
  residues processed: 158
  average time/residue: 0.5744
  time to fit residues: 97.0000
Evaluate side-chains
  157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 110 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.103286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.076065 restraints weight = 14947.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 2.09
r_work: 0.2628 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2493 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9174
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10763  Z= 0.187
  Angle     :  0.634  12.315  14575  Z= 0.324
  Chirality :  0.043   0.161   1662
  Planarity :  0.004   0.058   1827
  Dihedral  :  4.588  49.876   1467
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.20 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.18 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    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:  0.84 (0.24), residues: 1308
  helix:  1.81 (0.20), residues: 679
  sheet:  0.33 (0.36), residues: 194
  loop : -1.38 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 550 
 TYR   0.012   0.001   TYR A 581 
 PHE   0.019   0.002   PHE B 493 
 TRP   0.012   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00457 /  0.19 (10760)
  covalent geometry    : angle       0.63373 /  0.32 (14569)
  SS BOND              : bond        0.00658 /  0.45 (    3)
  SS BOND              : angle       1.61823 /  1.09 (    6)
  hydrogen bonds       : bond        0.05798 /  3.78 (  574)
  hydrogen bonds       : angle       3.93923 /  2.79 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3467.97 seconds
wall clock time: 59 minutes 54.78 seconds (3594.78 seconds total)