Starting phenix.real_space_refine
on Wed Sep 17 19:57:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9inh_60707/09_2025/9inh_60707.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9inh_60707/09_2025/9inh_60707.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9inh_60707/09_2025/9inh_60707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9inh_60707/09_2025/9inh_60707.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9inh_60707/09_2025/9inh_60707.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9inh_60707/09_2025/9inh_60707.cif"
  }
  resolution = 3.68
  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=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     P      28      5.49       5
     S      42      5.16       5
     C    7298      2.51       5
     N    1670      2.21       5
     O    1895      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10933
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 5030
          Classifications: {'peptide': 606}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 585}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 5059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 609, 5059
          Classifications: {'peptide': 609}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 588}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 422
          Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 6, 'IHP': 1, 'PLM': 1, 'PO4': 5}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
    Chain: "D"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 422
          Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 6, 'IHP': 1, 'PLM': 1, 'PO4': 5}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
  Time building chain proxies: 3.08, per 1000 atoms: 0.28
  Number of scatterers: 10933
  At special positions: 0
  Unit cell: (109.08, 96.152, 101, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P      28     15.00
     O    1895      8.00
     N    1670      7.00
     C    7298      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 415 " - pdb=" SG  CYS D 440 " 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: 0.93
  Conformation dependent library (CDL) restraints added in 402.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2332

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 0 sheets defined
      79.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 10
    Processing helix  chain 'A' and resid 12 through 17
      removed outlier: 4.409A  pdb=" N   LYS A  17 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 34
    Processing helix  chain 'A' and resid 43 through 103
    Processing helix  chain 'A' and resid 119 through 165
    Processing helix  chain 'A' and resid 173 through 180
    Processing helix  chain 'A' and resid 183 through 188
      removed outlier: 3.813A  pdb=" N   CYS A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 206
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.609A  pdb=" N   ALA A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 257
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.377A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 312 through 336
      removed outlier: 3.855A  pdb=" N   ILE A 319 " --> pdb=" O   HIS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 361
      removed outlier: 3.590A  pdb=" N   TYR A 352 " --> pdb=" O   PRO A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 384 through 387
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.823A  pdb=" N   ASN A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 3.706A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 446 through 471
      Proline residue:  A 455  - end of helix
      removed outlier: 3.560A  pdb=" N   PHE A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 4.196A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 503
      removed outlier: 4.582A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 524
      removed outlier: 4.096A  pdb=" N   ILE A 520 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 572
      removed outlier: 3.868A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 584
      removed outlier: 3.650A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   SER A 581 " --> pdb=" O   ILE A 577 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 619
      Proline residue:  A 598  - end of helix
      removed outlier: 3.732A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 10
    Processing helix  chain 'D' and resid 12 through 16
    Processing helix  chain 'D' and resid 21 through 34
      removed outlier: 3.545A  pdb=" N   ALA D  32 " --> pdb=" O   MET D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 103
      removed outlier: 3.576A  pdb=" N   SER D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 168
      removed outlier: 4.009A  pdb=" N   ASN D 152 " --> pdb=" O   TYR D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 179
    Processing helix  chain 'D' and resid 183 through 188
    Processing helix  chain 'D' and resid 189 through 205
      removed outlier: 3.557A  pdb=" N   GLN D 193 " --> pdb=" O   LYS D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 218
    Processing helix  chain 'D' and resid 230 through 258
      removed outlier: 3.811A  pdb=" N   ARG D 236 " --> pdb=" O   TRP D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 296
      removed outlier: 4.436A  pdb=" N   GLY D 274 " --> pdb=" O   ARG D 270 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   GLY D 275 " --> pdb=" O   ILE D 271 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE D 276 " --> pdb=" O   TYR D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 303
      removed outlier: 4.083A  pdb=" N   ILE D 302 " --> pdb=" O   ASN D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 337
      removed outlier: 3.773A  pdb=" N   ILE D 319 " --> pdb=" O   HIS D 315 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 343 through 345
      No H-bonds generated for 'chain 'D' and resid 343 through 345'
    Processing helix  chain 'D' and resid 346 through 360
    Processing helix  chain 'D' and resid 367 through 383
    Processing helix  chain 'D' and resid 384 through 387
      removed outlier: 3.511A  pdb=" N   HIS D 387 " --> pdb=" O   ALA D 384 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 384 through 387'
    Processing helix  chain 'D' and resid 390 through 403
      removed outlier: 4.091A  pdb=" N   ASN D 401 " --> pdb=" O   ALA D 397 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER D 402 " --> pdb=" O   ASP D 398 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 420
      removed outlier: 3.739A  pdb=" N   LEU D 407 " --> pdb=" O   LEU D 403 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 445
      No H-bonds generated for 'chain 'D' and resid 443 through 445'
    Processing helix  chain 'D' and resid 446 through 451
    Processing helix  chain 'D' and resid 453 through 471
    Processing helix  chain 'D' and resid 472 through 477
      removed outlier: 4.088A  pdb=" N   HIS D 476 " --> pdb=" O   ARG D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 477 through 503
      removed outlier: 4.569A  pdb=" N   THR D 486 " --> pdb=" O   LYS D 482 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   PHE D 487 " --> pdb=" O   TYR D 483 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE D 488 " --> pdb=" O   SER D 484 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 505 through 522
      removed outlier: 3.865A  pdb=" N   VAL D 509 " --> pdb=" O   SER D 505 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR D 512 " --> pdb=" O   MET D 508 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU D 513 " --> pdb=" O   VAL D 509 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 523 through 532
      removed outlier: 3.823A  pdb=" N   ASP D 529 " --> pdb=" O   THR D 525 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 555 through 570
      removed outlier: 3.889A  pdb=" N   TYR D 559 " --> pdb=" O   GLN D 555 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 571 through 580
      removed outlier: 4.360A  pdb=" N   ILE D 575 " --> pdb=" O   PHE D 571 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN D 576 " --> pdb=" O   ALA D 572 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 587 through 619
      removed outlier: 3.529A  pdb=" N   ILE D 591 " --> pdb=" O   HIS D 587 " (cutoff:3.500A)
      Proline residue:  D 598  - end of helix
      removed outlier: 3.588A  pdb=" N   PHE D 609 " --> pdb=" O   PHE D 605 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE D 610 " --> pdb=" O   VAL D 606 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU D 613 " --> pdb=" O   PHE D 609 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    2076 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: 1.64

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1716
        1.32 -     1.45: 3069
        1.45 -     1.57: 6370
        1.57 -     1.69: 24
        1.69 -     1.82: 60
  Bond restraints: 11239
  Sorted by residual:
  bond pdb=" O3  PO4 A 814 "
       pdb=" P   PO4 A 814 "
    ideal  model  delta    sigma   weight residual
    1.569  1.507  0.062 2.00e-02 2.50e+03 9.50e+00
  bond pdb=" O3  PO4 D 805 "
       pdb=" P   PO4 D 805 "
    ideal  model  delta    sigma   weight residual
    1.569  1.507  0.062 2.00e-02 2.50e+03 9.47e+00
  bond pdb=" O3  PO4 A 812 "
       pdb=" P   PO4 A 812 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.41e+00
  bond pdb=" O3  PO4 D 804 "
       pdb=" P   PO4 D 804 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.34e+00
  bond pdb=" O3  PO4 D 807 "
       pdb=" P   PO4 D 807 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.34e+00
  ... (remaining 11234 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 14768
        1.90 -     3.80: 359
        3.80 -     5.71: 74
        5.71 -     7.61: 20
        7.61 -     9.51: 8
  Bond angle restraints: 15229
  Sorted by residual:
  angle pdb=" N   VAL A 341 "
        pdb=" CA  VAL A 341 "
        pdb=" C   VAL A 341 "
      ideal   model   delta    sigma   weight residual
     113.53  108.92    4.61 9.80e-01 1.04e+00 2.21e+01
  angle pdb=" N   ASP A 174 "
        pdb=" CA  ASP A 174 "
        pdb=" C   ASP A 174 "
      ideal   model   delta    sigma   weight residual
     112.54  107.82    4.72 1.22e+00 6.72e-01 1.50e+01
  angle pdb=" N   ILE D 520 "
        pdb=" CA  ILE D 520 "
        pdb=" C   ILE D 520 "
      ideal   model   delta    sigma   weight residual
     113.42  109.14    4.28 1.17e+00 7.31e-01 1.34e+01
  angle pdb=" N   LYS D  26 "
        pdb=" CA  LYS D  26 "
        pdb=" C   LYS D  26 "
      ideal   model   delta    sigma   weight residual
     111.28  107.38    3.90 1.09e+00 8.42e-01 1.28e+01
  angle pdb=" CA  MET D 489 "
        pdb=" C   MET D 489 "
        pdb=" O   MET D 489 "
      ideal   model   delta    sigma   weight residual
     120.82  117.19    3.63 1.05e+00 9.07e-01 1.20e+01
  ... (remaining 15224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.80: 6846
       33.80 -    67.60: 354
       67.60 -   101.40: 27
      101.40 -   135.21: 27
      135.21 -   169.01: 9
  Dihedral angle restraints: 7263
    sinusoidal: 3664
      harmonic: 3599
  Sorted by residual:
  dihedral pdb=" O14 IHP D 801 "
           pdb=" C4  IHP D 801 "
           pdb=" C5  IHP D 801 "
           pdb=" O15 IHP D 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.79  116.22 -169.01     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" O14 IHP A 801 "
           pdb=" C4  IHP A 801 "
           pdb=" C5  IHP A 801 "
           pdb=" O15 IHP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.79  115.01 -167.80     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" C6  IHP A 801 "
           pdb=" C1  IHP A 801 "
           pdb=" C2  IHP A 801 "
           pdb=" O12 IHP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      61.05  -97.44  158.49     1      3.00e+01 1.11e-03 2.06e+01
  ... (remaining 7260 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.992: 1633
       0.992 -    1.984: 0
       1.984 -    2.976: 0
       2.976 -    3.968: 0
       3.968 -    4.961: 8
  Chirality restraints: 1641
  Sorted by residual:
  chirality pdb=" C2  IHP D 801 "
            pdb=" C1  IHP D 801 "
            pdb=" C3  IHP D 801 "
            pdb=" O12 IHP D 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.44   -4.96 2.00e-01 2.50e+01 6.15e+02
  chirality pdb=" C2  IHP A 801 "
            pdb=" C1  IHP A 801 "
            pdb=" C3  IHP A 801 "
            pdb=" O12 IHP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.44   -4.96 2.00e-01 2.50e+01 6.14e+02
  chirality pdb=" C6  IHP A 801 "
            pdb=" C1  IHP A 801 "
            pdb=" C5  IHP A 801 "
            pdb=" O16 IHP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50    2.35   -4.85 2.00e-01 2.50e+01 5.88e+02
  ... (remaining 1638 not shown)

  Planarity restraints: 1777
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 466 "    0.261 9.50e-02 1.11e+02   1.17e-01 8.43e+00
        pdb=" NE  ARG D 466 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 466 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 466 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 466 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  73 "   -0.009 2.00e-02 2.50e+03   1.60e-02 5.12e+00
        pdb=" CG  TYR D  73 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  73 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  73 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  73 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  73 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  73 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D  73 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 416 "    0.014 2.00e-02 2.50e+03   1.66e-02 4.83e+00
        pdb=" CG  PHE D 416 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 416 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 416 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 416 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 416 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 416 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1774 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1953
        2.76 -     3.30: 11375
        3.30 -     3.83: 18895
        3.83 -     4.37: 22388
        4.37 -     4.90: 36539
  Nonbonded interactions: 91150
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 545 "
            pdb=" OH  TYR D 560 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" N   GLU A 543 "
            pdb=" OE1 GLU A 543 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   ASP D  43 "
            pdb=" OG1 THR D  46 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ARG A 122 "
            pdb=" ND1 HIS A 125 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OG1 THR A 545 "
            pdb=" OH  TYR A 560 "
     model   vdw
     2.283 3.040
  ... (remaining 91145 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 207 or resid 211 through 801 or resid 810))
  selection = (chain 'D' and (resid 1 through 165 or resid 172 through 801 or resid 810))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.580
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  11241  Z= 0.284
  Angle     :  0.757   9.511  15233  Z= 0.403
  Chirality :  0.340   4.961   1641
  Planarity :  0.005   0.117   1777
  Dihedral  : 20.998 169.008   4925
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.13 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.24), residues: 1203
  helix:  0.83 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop : -1.17 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 176 
 TYR   0.038   0.002   TYR D  73 
 PHE   0.038   0.002   PHE D 416 
 TRP   0.019   0.001   TRP A 175 
 HIS   0.012   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 (11239)
  covalent geometry    : angle       0.75725 (15229)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.58570 (    4)
  hydrogen bonds       : bond        0.14715 (  695)
  hydrogen bonds       : angle       6.55063 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7543 (mmm160)
REVERT: A  559 TYR cc_start: 0.7589 (m-80) cc_final: 0.6917 (m-80)
REVERT: D    1 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6929 (ppp)
REVERT: D   25 PHE cc_start: 0.6667 (m-80) cc_final: 0.6318 (m-80)
  outliers start: 13
  outliers final: 5
  residues processed: 131
  average time/residue: 0.1238
  time to fit residues: 22.4763
Evaluate side-chains
  118 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  463 CYS
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0670
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0020
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.1642

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 GLN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.213527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.160623 restraints weight = 14138.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.159082 restraints weight = 12590.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.160989 restraints weight = 11028.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.161661 restraints weight = 8029.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.162089 restraints weight = 7596.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11241  Z= 0.139
  Angle     :  0.660  15.130  15233  Z= 0.311
  Chirality :  0.045   0.476   1641
  Planarity :  0.004   0.045   1777
  Dihedral  : 16.328 147.723   2557
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.63 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.24), residues: 1203
  helix:  1.17 (0.17), residues: 909
  sheet:  None (None), residues: 0
  loop : -1.06 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 371 
 TYR   0.021   0.001   TYR A 368 
 PHE   0.029   0.002   PHE A 135 
 TRP   0.010   0.001   TRP A 607 
 HIS   0.010   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11239)
  covalent geometry    : angle       0.66013 (15229)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       0.54680 (    4)
  hydrogen bonds       : bond        0.04865 (  695)
  hydrogen bonds       : angle       5.01303 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7280 (m-10) cc_final: 0.7001 (m-10)
REVERT: A   83 ARG cc_start: 0.8075 (tpp-160) cc_final: 0.7692 (mmm160)
REVERT: A   84 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6506 (m-10)
REVERT: A  292 TRP cc_start: 0.8507 (m-10) cc_final: 0.8248 (m-10)
REVERT: A  559 TYR cc_start: 0.7487 (m-80) cc_final: 0.6849 (m-80)
  outliers start: 24
  outliers final: 5
  residues processed: 141
  average time/residue: 0.1123
  time to fit residues: 22.2863
Evaluate side-chains
  120 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue   54 PHE
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  463 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 117 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 12 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.208264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.153739 restraints weight = 14353.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.150707 restraints weight = 13953.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.152877 restraints weight = 11909.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.153786 restraints weight = 8359.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.153834 restraints weight = 7511.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11241  Z= 0.201
  Angle     :  0.655  10.687  15233  Z= 0.319
  Chirality :  0.045   0.414   1641
  Planarity :  0.004   0.057   1777
  Dihedral  : 15.400 143.839   2547
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.35 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.24), residues: 1203
  helix:  1.13 (0.17), residues: 913
  sheet:  None (None), residues: 0
  loop : -0.96 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 448 
 TYR   0.021   0.002   TYR D 368 
 PHE   0.031   0.002   PHE A 135 
 TRP   0.014   0.001   TRP A 514 
 HIS   0.011   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (11239)
  covalent geometry    : angle       0.65498 (15229)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       0.77509 (    4)
  hydrogen bonds       : bond        0.04760 (  695)
  hydrogen bonds       : angle       4.88167 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7456 (m-10) cc_final: 0.7058 (m-10)
REVERT: A   84 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6568 (m-10)
REVERT: A  559 TYR cc_start: 0.7720 (m-80) cc_final: 0.7178 (m-80)
REVERT: D  157 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7194 (mmt180)
REVERT: D  302 ILE cc_start: 0.8563 (mt) cc_final: 0.8111 (mm)
REVERT: D  508 MET cc_start: 0.5638 (tpp) cc_final: 0.5417 (tpp)
  outliers start: 33
  outliers final: 19
  residues processed: 148
  average time/residue: 0.0990
  time to fit residues: 20.9583
Evaluate side-chains
  133 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue   54 PHE
Chi-restraints excluded: chain D residue  304 GLU
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 70 optimal weight:    7.9990
   chunk 103 optimal weight:    0.2980
   chunk 54 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0030
   chunk 9 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
A 125 HIS
A 127 ASN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.211526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.157070 restraints weight = 14310.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.155731 restraints weight = 12982.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.157749 restraints weight = 10803.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.158436 restraints weight = 8188.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.158554 restraints weight = 7295.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11241  Z= 0.136
  Angle     :  0.580  10.850  15233  Z= 0.288
  Chirality :  0.043   0.404   1641
  Planarity :  0.004   0.046   1777
  Dihedral  : 14.766 140.806   2546
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.81 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.24), residues: 1203
  helix:  1.22 (0.17), residues: 917
  sheet:  None (None), residues: 0
  loop : -0.94 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 157 
 TYR   0.023   0.002   TYR D  73 
 PHE   0.033   0.001   PHE D 135 
 TRP   0.013   0.001   TRP A 514 
 HIS   0.011   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (11239)
  covalent geometry    : angle       0.57997 (15229)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.59798 (    4)
  hydrogen bonds       : bond        0.04317 (  695)
  hydrogen bonds       : angle       4.66824 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7353 (m-10) cc_final: 0.6949 (m-10)
REVERT: A   83 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7724 (mmm160)
REVERT: A   84 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6558 (m-10)
REVERT: A  157 ARG cc_start: 0.7393 (mmt180) cc_final: 0.7014 (mmt180)
REVERT: A  292 TRP cc_start: 0.8495 (m-10) cc_final: 0.8287 (m-10)
REVERT: A  508 MET cc_start: 0.4565 (tpp) cc_final: 0.4171 (tpp)
REVERT: D  302 ILE cc_start: 0.8495 (mt) cc_final: 0.8047 (mm)
  outliers start: 34
  outliers final: 19
  residues processed: 148
  average time/residue: 0.0946
  time to fit residues: 20.0812
Evaluate side-chains
  139 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0570
   chunk 41 optimal weight:    1.9990
   chunk 118 optimal weight:    0.6980
   chunk 59 optimal weight:    0.1980
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 119 optimal weight:    0.3980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.211940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.157595 restraints weight = 14161.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.154941 restraints weight = 13033.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.157320 restraints weight = 11199.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.158003 restraints weight = 8110.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.158165 restraints weight = 7452.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11241  Z= 0.127
  Angle     :  0.562  10.677  15233  Z= 0.279
  Chirality :  0.043   0.433   1641
  Planarity :  0.004   0.071   1777
  Dihedral  : 14.354 138.401   2546
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.92 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.24), residues: 1203
  helix:  1.31 (0.17), residues: 917
  sheet:  None (None), residues: 0
  loop : -0.94 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 157 
 TYR   0.027   0.002   TYR D  19 
 PHE   0.018   0.001   PHE D 185 
 TRP   0.013   0.001   TRP A 514 
 HIS   0.011   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11239)
  covalent geometry    : angle       0.56208 (15229)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       0.55542 (    4)
  hydrogen bonds       : bond        0.04188 (  695)
  hydrogen bonds       : angle       4.57216 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7418 (m-10) cc_final: 0.7041 (m-10)
REVERT: A   83 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7616 (mmm160)
REVERT: A   84 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6610 (m-10)
REVERT: A  292 TRP cc_start: 0.8489 (m-10) cc_final: 0.8261 (m-10)
REVERT: A  508 MET cc_start: 0.4776 (tpp) cc_final: 0.4488 (tpp)
REVERT: A  559 TYR cc_start: 0.7687 (m-80) cc_final: 0.7277 (m-80)
REVERT: D   25 PHE cc_start: 0.7347 (m-80) cc_final: 0.6698 (m-80)
REVERT: D   84 PHE cc_start: 0.7519 (m-80) cc_final: 0.7096 (m-10)
REVERT: D  302 ILE cc_start: 0.8521 (mt) cc_final: 0.8049 (mm)
  outliers start: 35
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1036
  time to fit residues: 22.3214
Evaluate side-chains
  148 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  248 ASN
Chi-restraints excluded: chain D residue  304 GLU
Chi-restraints excluded: chain D residue  328 CYS
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  532 MET
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  605 PHE
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0570
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.210200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.155452 restraints weight = 14255.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.152645 restraints weight = 13625.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.154869 restraints weight = 11598.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.155641 restraints weight = 7941.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.155811 restraints weight = 7512.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11241  Z= 0.157
  Angle     :  0.592   9.414  15233  Z= 0.294
  Chirality :  0.044   0.432   1641
  Planarity :  0.004   0.064   1777
  Dihedral  : 14.150 137.270   2546
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.39 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.24), residues: 1203
  helix:  1.32 (0.17), residues: 917
  sheet:  None (None), residues: 0
  loop : -1.00 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 157 
 TYR   0.027   0.002   TYR A  73 
 PHE   0.017   0.001   PHE A 185 
 TRP   0.014   0.001   TRP A 514 
 HIS   0.011   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (11239)
  covalent geometry    : angle       0.59216 (15229)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.58703 (    4)
  hydrogen bonds       : bond        0.04267 (  695)
  hydrogen bonds       : angle       4.58070 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7450 (m-10) cc_final: 0.7051 (m-10)
REVERT: A   83 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7738 (mmm160)
REVERT: A   84 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6651 (m-10)
REVERT: A  508 MET cc_start: 0.4871 (tpp) cc_final: 0.4625 (tpp)
REVERT: D   84 PHE cc_start: 0.7516 (m-80) cc_final: 0.7091 (m-10)
REVERT: D  302 ILE cc_start: 0.8555 (mt) cc_final: 0.8088 (mm)
  outliers start: 33
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1061
  time to fit residues: 21.7638
Evaluate side-chains
  137 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  328 CYS
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  532 MET
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  605 PHE
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 89 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0570
   chunk 117 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.211335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.157218 restraints weight = 14196.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.154330 restraints weight = 13413.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.156527 restraints weight = 11475.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.157260 restraints weight = 7901.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.157444 restraints weight = 7544.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11241  Z= 0.134
  Angle     :  0.561   8.501  15233  Z= 0.283
  Chirality :  0.042   0.382   1641
  Planarity :  0.004   0.075   1777
  Dihedral  : 13.895 135.809   2546
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.11 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.24), residues: 1203
  helix:  1.38 (0.17), residues: 916
  sheet:  None (None), residues: 0
  loop : -0.97 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 157 
 TYR   0.029   0.002   TYR A  73 
 PHE   0.018   0.001   PHE A  25 
 TRP   0.018   0.001   TRP A 514 
 HIS   0.012   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11239)
  covalent geometry    : angle       0.56121 (15229)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.53977 (    4)
  hydrogen bonds       : bond        0.04102 (  695)
  hydrogen bonds       : angle       4.50589 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 129
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7426 (m-10) cc_final: 0.7037 (m-10)
REVERT: A   83 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7622 (mmm160)
REVERT: A   84 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6644 (m-10)
REVERT: A  326 LEU cc_start: 0.8169 (mt) cc_final: 0.7957 (mt)
REVERT: D   84 PHE cc_start: 0.7474 (m-80) cc_final: 0.7096 (m-10)
REVERT: D  302 ILE cc_start: 0.8545 (mt) cc_final: 0.8077 (mm)
  outliers start: 38
  outliers final: 27
  residues processed: 155
  average time/residue: 0.1121
  time to fit residues: 24.4447
Evaluate side-chains
  147 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  248 ASN
Chi-restraints excluded: chain D residue  328 CYS
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  532 MET
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  605 PHE
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:    0.6980
   chunk 112 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 GLN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN
** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.204308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.148509 restraints weight = 14157.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.144725 restraints weight = 12484.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.147091 restraints weight = 10801.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.147876 restraints weight = 7504.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.148077 restraints weight = 7154.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11241  Z= 0.233
  Angle     :  0.675  10.520  15233  Z= 0.335
  Chirality :  0.044   0.300   1641
  Planarity :  0.005   0.079   1777
  Dihedral  : 14.150 136.930   2546
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.67 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.24), residues: 1203
  helix:  1.26 (0.17), residues: 909
  sheet:  None (None), residues: 0
  loop : -0.79 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 157 
 TYR   0.024   0.002   TYR A 368 
 PHE   0.025   0.002   PHE A 416 
 TRP   0.019   0.002   TRP A 514 
 HIS   0.018   0.002   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (11239)
  covalent geometry    : angle       0.67520 (15229)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.78910 (    4)
  hydrogen bonds       : bond        0.04594 (  695)
  hydrogen bonds       : angle       4.71195 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7474 (m-10) cc_final: 0.7077 (m-10)
REVERT: A   83 ARG cc_start: 0.8121 (tpp-160) cc_final: 0.7755 (mmm160)
REVERT: A   84 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6738 (m-10)
REVERT: A  559 TYR cc_start: 0.7858 (m-80) cc_final: 0.7360 (m-80)
REVERT: D   84 PHE cc_start: 0.7555 (m-80) cc_final: 0.7170 (m-10)
REVERT: D  573 TRP cc_start: 0.6699 (m100) cc_final: 0.6231 (m100)
  outliers start: 36
  outliers final: 24
  residues processed: 151
  average time/residue: 0.1098
  time to fit residues: 23.6760
Evaluate side-chains
  142 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  248 ASN
Chi-restraints excluded: chain D residue  328 CYS
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  532 MET
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 76 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   chunk 64 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.207284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.151862 restraints weight = 14015.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.148583 restraints weight = 12332.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.150865 restraints weight = 10331.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.151702 restraints weight = 7345.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.151926 restraints weight = 6841.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11241  Z= 0.147
  Angle     :  0.608   8.579  15233  Z= 0.305
  Chirality :  0.041   0.280   1641
  Planarity :  0.004   0.083   1777
  Dihedral  : 13.984 136.862   2546
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.69 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.24), residues: 1203
  helix:  1.32 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.90 (0.38), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 157 
 TYR   0.033   0.002   TYR A  73 
 PHE   0.023   0.002   PHE A 416 
 TRP   0.019   0.001   TRP A 514 
 HIS   0.016   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11239)
  covalent geometry    : angle       0.60791 (15229)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       0.66727 (    4)
  hydrogen bonds       : bond        0.04289 (  695)
  hydrogen bonds       : angle       4.58977 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7378 (m-10) cc_final: 0.7009 (m-10)
REVERT: A   83 ARG cc_start: 0.8117 (tpp-160) cc_final: 0.7765 (mmm160)
REVERT: A   84 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6714 (m-10)
REVERT: D   84 PHE cc_start: 0.7500 (m-80) cc_final: 0.7126 (m-10)
REVERT: D  573 TRP cc_start: 0.6576 (m100) cc_final: 0.6110 (m100)
  outliers start: 31
  outliers final: 26
  residues processed: 141
  average time/residue: 0.1074
  time to fit residues: 21.7997
Evaluate side-chains
  145 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  248 ASN
Chi-restraints excluded: chain D residue  328 CYS
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  532 MET
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 94 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0040
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.209937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.155758 restraints weight = 14245.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.153042 restraints weight = 13556.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.155220 restraints weight = 11267.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.155957 restraints weight = 7942.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.156168 restraints weight = 7537.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11241  Z= 0.150
  Angle     :  0.614   8.555  15233  Z= 0.308
  Chirality :  0.041   0.271   1641
  Planarity :  0.004   0.072   1777
  Dihedral  : 13.862 136.168   2546
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.61 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.24), residues: 1203
  helix:  1.36 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.89 (0.38), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 176 
 TYR   0.027   0.002   TYR A 368 
 PHE   0.024   0.002   PHE A  25 
 TRP   0.019   0.001   TRP A 514 
 HIS   0.016   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11239)
  covalent geometry    : angle       0.61402 (15229)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.68668 (    4)
  hydrogen bonds       : bond        0.04294 (  695)
  hydrogen bonds       : angle       4.56308 ( 2076)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.7303 (m-10) cc_final: 0.6965 (m-10)
REVERT: A   83 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7597 (mmm160)
REVERT: A   84 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6707 (m-10)
REVERT: D   84 PHE cc_start: 0.7492 (m-80) cc_final: 0.7129 (m-10)
  outliers start: 25
  outliers final: 24
  residues processed: 138
  average time/residue: 0.1118
  time to fit residues: 21.9153
Evaluate side-chains
  142 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  328 CYS
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  375 LEU
Chi-restraints excluded: chain D residue  439 ILE
Chi-restraints excluded: chain D residue  441 HIS
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  515 ILE
Chi-restraints excluded: chain D residue  532 MET
Chi-restraints excluded: chain D residue  574 THR
Chi-restraints excluded: chain D residue  609 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 32 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.207801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.152346 restraints weight = 14020.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.149109 restraints weight = 12261.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.151309 restraints weight = 10441.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.152179 restraints weight = 7368.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.152378 restraints weight = 6809.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11241  Z= 0.150
  Angle     :  0.616   8.550  15233  Z= 0.309
  Chirality :  0.041   0.266   1641
  Planarity :  0.004   0.042   1777
  Dihedral  : 13.754 135.577   2546
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.80 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.24), residues: 1203
  helix:  1.36 (0.17), residues: 913
  sheet:  None (None), residues: 0
  loop : -0.88 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 176 
 TYR   0.029   0.002   TYR D 368 
 PHE   0.024   0.002   PHE A  25 
 TRP   0.018   0.001   TRP A 514 
 HIS   0.015   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11239)
  covalent geometry    : angle       0.61622 (15229)
  SS BOND              : bond        0.00165 (    2)
  SS BOND              : angle       0.67176 (    4)
  hydrogen bonds       : bond        0.04264 (  695)
  hydrogen bonds       : angle       4.53980 ( 2076)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1776.05 seconds
wall clock time: 31 minutes 43.36 seconds (1903.36 seconds total)