Starting phenix.real_space_refine
on Wed Mar  4 00:16:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oz1_13118/03_2026/7oz1_13118.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oz1_13118/03_2026/7oz1_13118.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oz1_13118/03_2026/7oz1_13118.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oz1_13118/03_2026/7oz1_13118.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oz1_13118/03_2026/7oz1_13118.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oz1_13118/03_2026/7oz1_13118.cif"
  }
  resolution = 4.0
  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=   0.002
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       8      5.49       5
     S      68      5.16       5
     C    5864      2.51       5
     N    1414      2.21       5
     O    1588      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8942
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 544, 4257
          Classifications: {'peptide': 544}
          Link IDs: {'PTRANS': 19, 'TRANS': 524}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 544, 4257
          Classifications: {'peptide': 544}
          Link IDs: {'PTRANS': 19, 'TRANS': 524}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 214
          Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 214
          Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
  Time building chain proxies: 2.34, per 1000 atoms: 0.26
  Number of scatterers: 8942
  At special positions: 0
  Unit cell: (78.54, 104.94, 123.42, 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      68     16.00
     P       8     15.00
     O    1588      8.00
     N    1414      7.00
     C    5864      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 611 " - pdb=" SG  CYS A 617 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 611 " - pdb=" SG  CYS B 617 " distance=2.04

  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: 0.78
  Conformation dependent library (CDL) restraints added in 370.1 milliseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      60.5% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 132
    Processing helix  chain 'A' and resid 154 through 157
    Processing helix  chain 'A' and resid 173 through 186
      removed outlier: 3.748A  pdb=" N   LYS A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 205
      removed outlier: 3.924A  pdb=" N   GLU A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.633A  pdb=" N   ALA A 210 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ASN A 211 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 211'
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 4.046A  pdb=" N   GLU A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   VAL A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 264
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 303 through 310
      removed outlier: 3.857A  pdb=" N   ASP A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
      removed outlier: 3.607A  pdb=" N   SER A 330 " --> pdb=" O   MET A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 344
      removed outlier: 4.673A  pdb=" N   ARG A 342 " --> pdb=" O   SER A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 406
    Processing helix  chain 'A' and resid 411 through 429
    Processing helix  chain 'A' and resid 439 through 475
      removed outlier: 3.887A  pdb=" N   MET A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      Proline residue:  A 460  - end of helix
      Proline residue:  A 466  - end of helix
    Processing helix  chain 'A' and resid 482 through 513
      removed outlier: 3.628A  pdb=" N   TYR A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
      Proline residue:  A 496  - end of helix
      Proline residue:  A 502  - end of helix
    Processing helix  chain 'A' and resid 518 through 547
      removed outlier: 4.322A  pdb=" N   PHE A 522 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 560
      Proline residue:  A 558  - end of helix
    Processing helix  chain 'A' and resid 560 through 567
      removed outlier: 4.139A  pdb=" N   VAL A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 580
      No H-bonds generated for 'chain 'A' and resid 578 through 580'
    Processing helix  chain 'A' and resid 581 through 586
      removed outlier: 3.697A  pdb=" N   SER A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR A 586 " --> pdb=" O   GLN A 582 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 581 through 586'
    Processing helix  chain 'A' and resid 588 through 602
      removed outlier: 3.779A  pdb=" N   TYR A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 629
    Processing helix  chain 'A' and resid 636 through 664
      removed outlier: 3.740A  pdb=" N   PHE A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
    Processing helix  chain 'B' and resid 154 through 157
    Processing helix  chain 'B' and resid 173 through 186
      removed outlier: 3.748A  pdb=" N   LYS B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 205
      removed outlier: 3.924A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 211
      removed outlier: 3.632A  pdb=" N   ALA B 210 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASN B 211 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 207 through 211'
    Processing helix  chain 'B' and resid 218 through 232
      removed outlier: 4.046A  pdb=" N   GLU B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   VAL B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 303 through 310
      removed outlier: 3.857A  pdb=" N   ASP B 310 " --> pdb=" O   PRO B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
      removed outlier: 3.607A  pdb=" N   SER B 330 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 344
      removed outlier: 4.673A  pdb=" N   ARG B 342 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 406
    Processing helix  chain 'B' and resid 411 through 429
    Processing helix  chain 'B' and resid 439 through 475
      removed outlier: 3.887A  pdb=" N   MET B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)
      Proline residue:  B 460  - end of helix
      Proline residue:  B 466  - end of helix
    Processing helix  chain 'B' and resid 482 through 513
      removed outlier: 3.628A  pdb=" N   TYR B 486 " --> pdb=" O   SER B 482 " (cutoff:3.500A)
      Proline residue:  B 496  - end of helix
      Proline residue:  B 502  - end of helix
    Processing helix  chain 'B' and resid 518 through 547
      removed outlier: 4.322A  pdb=" N   PHE B 522 " --> pdb=" O   ASP B 518 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL B 523 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA B 545 " --> pdb=" O   LEU B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 560
      Proline residue:  B 558  - end of helix
    Processing helix  chain 'B' and resid 560 through 567
      removed outlier: 4.139A  pdb=" N   VAL B 564 " --> pdb=" O   THR B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 580
      No H-bonds generated for 'chain 'B' and resid 578 through 580'
    Processing helix  chain 'B' and resid 581 through 586
      removed outlier: 3.696A  pdb=" N   SER B 585 " --> pdb=" O   LEU B 581 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TYR B 586 " --> pdb=" O   GLN B 582 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 581 through 586'
    Processing helix  chain 'B' and resid 588 through 602
      removed outlier: 3.779A  pdb=" N   TYR B 592 " --> pdb=" O   SER B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 629
    Processing helix  chain 'B' and resid 636 through 664
      removed outlier: 3.741A  pdb=" N   PHE B 640 " --> pdb=" O   LEU B 636 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 99
      removed outlier: 5.219A  pdb=" N   ILE A 104 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99
      removed outlier: 4.209A  pdb=" N   LEU A  82 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   LYS A 140 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161
      removed outlier: 6.752A  pdb=" N   CYS A 160 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLN A 286 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291
      removed outlier: 7.006A  pdb=" N   VAL A 289 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 99
      removed outlier: 5.219A  pdb=" N   ILE B 104 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 99
      removed outlier: 4.209A  pdb=" N   LEU B  82 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   LYS B 140 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161
      removed outlier: 6.751A  pdb=" N   CYS B 160 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLN B 286 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291
      removed outlier: 7.007A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1338 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: 1.86

  Time building geometry restraints manager: 1.06 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: 1397
        1.32 -     1.45: 2380
        1.45 -     1.57: 5245
        1.57 -     1.70: 14
        1.70 -     1.83: 110
  Bond restraints: 9146
  Sorted by residual:
  bond pdb=" C4  ATP A 701 "
       pdb=" C5  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.90e+01
  bond pdb=" C4  ATP B 701 "
       pdb=" C5  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.89e+01
  bond pdb=" C5  ATP A 701 "
       pdb=" C6  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.481 -0.072 1.00e-02 1.00e+04 5.14e+01
  bond pdb=" C5  ATP B 701 "
       pdb=" C6  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.480 -0.071 1.00e-02 1.00e+04 5.06e+01
  bond pdb=" C8  ATP A 701 "
       pdb=" N7  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.310  1.357 -0.047 1.00e-02 1.00e+04 2.20e+01
  ... (remaining 9141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 12322
        3.66 -     7.33: 72
        7.33 -    10.99: 8
       10.99 -    14.65: 0
       14.65 -    18.31: 6
  Bond angle restraints: 12408
  Sorted by residual:
  angle pdb=" PB  ATP A 701 "
        pdb=" O3B ATP A 701 "
        pdb=" PG  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     139.87  123.04   16.83 1.00e+00 1.00e+00 2.83e+02
  angle pdb=" PB  ATP B 701 "
        pdb=" O3B ATP B 701 "
        pdb=" PG  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     139.87  123.04   16.83 1.00e+00 1.00e+00 2.83e+02
  angle pdb=" PA  ATP B 701 "
        pdb=" O3A ATP B 701 "
        pdb=" PB  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     136.83  120.56   16.27 1.00e+00 1.00e+00 2.65e+02
  angle pdb=" PA  ATP A 701 "
        pdb=" O3A ATP A 701 "
        pdb=" PB  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     136.83  120.59   16.24 1.00e+00 1.00e+00 2.64e+02
  angle pdb=" N   PRO A 276 "
        pdb=" CA  PRO A 276 "
        pdb=" C   PRO A 276 "
      ideal   model   delta    sigma   weight residual
     112.47   94.16   18.31 2.06e+00 2.36e-01 7.90e+01
  ... (remaining 12403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.15: 5712
       34.15 -    68.30: 156
       68.30 -   102.46: 14
      102.46 -   136.61: 0
      136.61 -   170.76: 6
  Dihedral angle restraints: 5888
    sinusoidal: 2746
      harmonic: 3142
  Sorted by residual:
  dihedral pdb=" CB  CYS A 611 "
           pdb=" SG  CYS A 611 "
           pdb=" SG  CYS A 617 "
           pdb=" CB  CYS A 617 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.47  -40.53     1      1.00e+01 1.00e-02 2.30e+01
  dihedral pdb=" CB  CYS B 611 "
           pdb=" SG  CYS B 611 "
           pdb=" SG  CYS B 617 "
           pdb=" CB  CYS B 617 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.49  -40.51     1      1.00e+01 1.00e-02 2.30e+01
  dihedral pdb=" C4  PEE B 706 "
           pdb=" O4P PEE B 706 "
           pdb=" P   PEE B 706 "
           pdb=" O2P PEE B 706 "
      ideal   model   delta sinusoidal    sigma   weight residual
     284.22  113.46  170.76     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 5885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1238
       0.070 -    0.140: 167
       0.140 -    0.210: 19
       0.210 -    0.280: 4
       0.280 -    0.350: 2
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CA  PRO A 276 "
            pdb=" N   PRO A 276 "
            pdb=" C   PRO A 276 "
            pdb=" CB  PRO A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    3.07   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  PRO B 276 "
            pdb=" N   PRO B 276 "
            pdb=" C   PRO B 276 "
            pdb=" CB  PRO B 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    3.07   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CBE Y01 B 702 "
            pdb=" CAP Y01 B 702 "
            pdb=" CBB Y01 B 702 "
            pdb=" CBI Y01 B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.29    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 277 "    0.017 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   SER B 277 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   SER B 277 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ALA B 278 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 277 "   -0.017 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   SER A 277 "    0.060 2.00e-02 2.50e+03
        pdb=" O   SER A 277 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA A 278 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 459 "    0.034 5.00e-02 4.00e+02   5.05e-02 4.09e+00
        pdb=" N   PRO A 460 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 460 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 460 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 119
        2.67 -     3.23: 8739
        3.23 -     3.78: 13178
        3.78 -     4.34: 17986
        4.34 -     4.90: 28954
  Nonbonded interactions: 68976
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 125 "
            pdb=" O1B ATP B 701 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OG  SER A 125 "
            pdb=" O1B ATP A 701 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OH  TYR B 297 "
            pdb=" O   LYS B 300 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OH  TYR A 297 "
            pdb=" O   LYS A 300 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" O   LEU B 550 "
            pdb=" OG1 THR B 554 "
     model   vdw
     2.251 3.040
  ... (remaining 68971 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 74 through 704)
  selection = (chain 'B' and resid 74 through 704)
}

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:             5.570
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.050
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
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   0.083   9148  Z= 0.371
  Angle     :  0.917  18.314  12412  Z= 0.584
  Chirality :  0.051   0.350   1430
  Planarity :  0.004   0.051   1490
  Dihedral  : 16.761 170.761   3870
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  7.51 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.23), residues: 1076
  helix: -1.39 (0.18), residues: 602
  sheet: -1.84 (0.63), residues: 74
  loop : -3.31 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 224 
 TYR   0.009   0.001   TYR B 481 
 PHE   0.012   0.002   PHE B 646 
 TRP   0.012   0.002   TRP B 480 
 HIS   0.002   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 9146)
  covalent geometry    : angle       0.91630 (12408)
  SS BOND              : bond        0.00889 (    2)
  SS BOND              : angle       2.10572 (    4)
  hydrogen bonds       : bond        0.11285 (  454)
  hydrogen bonds       : angle       5.31263 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 199
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8493 (tpp) cc_final: 0.8029 (tpt)
REVERT: A  259 MET cc_start: 0.8671 (ttm) cc_final: 0.8359 (ttm)
REVERT: A  492 MET cc_start: 0.7730 (mmm) cc_final: 0.7334 (mtp)
REVERT: A  511 TRP cc_start: 0.8125 (m100) cc_final: 0.7833 (m-10)
REVERT: A  609 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp)
REVERT: B  179 MET cc_start: 0.8477 (tpp) cc_final: 0.7954 (tpt)
REVERT: B  259 MET cc_start: 0.8654 (ttm) cc_final: 0.8327 (ttm)
REVERT: B  492 MET cc_start: 0.7721 (mmm) cc_final: 0.7368 (mtp)
REVERT: B  511 TRP cc_start: 0.8110 (m100) cc_final: 0.7852 (m-10)
REVERT: B  609 LEU cc_start: 0.8582 (tp) cc_final: 0.8366 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1027
  time to fit residues: 27.7322
Evaluate side-chains
  142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    0.0570
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4354

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 336 GLN
A 418 HIS
B 175 GLN
B 336 GLN
B 418 HIS
B 633 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.139240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.122305 restraints weight = 12463.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124789 restraints weight = 8234.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.126483 restraints weight = 5971.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127871 restraints weight = 4699.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.128886 restraints weight = 3854.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9148  Z= 0.128
  Angle     :  0.628   5.811  12412  Z= 0.310
  Chirality :  0.041   0.179   1430
  Planarity :  0.004   0.032   1490
  Dihedral  : 14.813 176.184   1896
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.56 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.25), residues: 1076
  helix:  0.01 (0.21), residues: 612
  sheet: -1.63 (0.58), residues: 74
  loop : -2.85 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 345 
 TYR   0.008   0.001   TYR B 134 
 PHE   0.015   0.002   PHE B 281 
 TRP   0.010   0.001   TRP A 480 
 HIS   0.003   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9146)
  covalent geometry    : angle       0.62752 (12408)
  SS BOND              : bond        0.00892 (    2)
  SS BOND              : angle       1.74027 (    4)
  hydrogen bonds       : bond        0.03811 (  454)
  hydrogen bonds       : angle       4.33274 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.7951 (mmm) cc_final: 0.7408 (mmm)
REVERT: A  179 MET cc_start: 0.8625 (tpp) cc_final: 0.8311 (tpt)
REVERT: A  298 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7766 (tmm-80)
REVERT: A  404 ILE cc_start: 0.8004 (tt) cc_final: 0.7629 (mt)
REVERT: A  407 ASP cc_start: 0.8179 (t0) cc_final: 0.7935 (t0)
REVERT: A  446 LEU cc_start: 0.8165 (tp) cc_final: 0.7840 (tp)
REVERT: A  492 MET cc_start: 0.7739 (mmm) cc_final: 0.7242 (mtp)
REVERT: A  511 TRP cc_start: 0.7885 (m100) cc_final: 0.7604 (m-10)
REVERT: A  609 LEU cc_start: 0.8484 (tp) cc_final: 0.8258 (tp)
REVERT: B  178 MET cc_start: 0.7939 (mmm) cc_final: 0.7340 (mmm)
REVERT: B  179 MET cc_start: 0.8606 (tpp) cc_final: 0.8181 (tpt)
REVERT: B  298 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.8110 (ttt180)
REVERT: B  404 ILE cc_start: 0.8017 (tt) cc_final: 0.7660 (mt)
REVERT: B  407 ASP cc_start: 0.8119 (t0) cc_final: 0.7881 (t0)
REVERT: B  446 LEU cc_start: 0.8132 (tp) cc_final: 0.7780 (tp)
REVERT: B  454 MET cc_start: 0.8143 (ttp) cc_final: 0.7939 (tmm)
REVERT: B  492 MET cc_start: 0.7737 (mmm) cc_final: 0.7256 (mtp)
REVERT: B  511 TRP cc_start: 0.7843 (m100) cc_final: 0.7595 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 161
  average time/residue: 0.0839
  time to fit residues: 19.0972
Evaluate side-chains
  141 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  467 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 320 ASN
A 418 HIS
B 418 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.136196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.119461 restraints weight = 12653.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.121873 restraints weight = 8352.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.123714 restraints weight = 6082.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.124961 restraints weight = 4745.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.125770 restraints weight = 3943.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9148  Z= 0.141
  Angle     :  0.594   5.676  12412  Z= 0.293
  Chirality :  0.041   0.143   1430
  Planarity :  0.004   0.030   1490
  Dihedral  : 14.005 172.998   1896
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.92 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.26), residues: 1076
  helix:  0.45 (0.21), residues: 616
  sheet: -1.62 (0.57), residues: 74
  loop : -2.61 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 345 
 TYR   0.008   0.001   TYR B 288 
 PHE   0.018   0.001   PHE B 281 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.007   0.001   HIS B 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9146)
  covalent geometry    : angle       0.59405 (12408)
  SS BOND              : bond        0.00673 (    2)
  SS BOND              : angle       1.40638 (    4)
  hydrogen bonds       : bond        0.03630 (  454)
  hydrogen bonds       : angle       4.15459 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8623 (tpp) cc_final: 0.8334 (tpt)
REVERT: A  404 ILE cc_start: 0.8033 (tt) cc_final: 0.7700 (mt)
REVERT: A  492 MET cc_start: 0.7672 (mmm) cc_final: 0.7207 (mtp)
REVERT: A  511 TRP cc_start: 0.7953 (m100) cc_final: 0.7621 (m-10)
REVERT: B  179 MET cc_start: 0.8605 (tpp) cc_final: 0.8214 (tpt)
REVERT: B  298 ARG cc_start: 0.8373 (tmm-80) cc_final: 0.8168 (ttt180)
REVERT: B  404 ILE cc_start: 0.8059 (tt) cc_final: 0.7725 (mt)
REVERT: B  492 MET cc_start: 0.7735 (mmm) cc_final: 0.7291 (mtp)
REVERT: B  511 TRP cc_start: 0.7919 (m100) cc_final: 0.7617 (m-10)
REVERT: B  609 LEU cc_start: 0.8265 (tp) cc_final: 0.8061 (tp)
  outliers start: 16
  outliers final: 14
  residues processed: 151
  average time/residue: 0.0704
  time to fit residues: 15.8797
Evaluate side-chains
  148 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  657 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 103 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
B 264 GLN
B 418 HIS
B 582 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.137536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.120929 restraints weight = 12812.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.123340 restraints weight = 8314.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.125183 restraints weight = 5993.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.126412 restraints weight = 4648.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.127263 restraints weight = 3831.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9148  Z= 0.113
  Angle     :  0.575   6.186  12412  Z= 0.281
  Chirality :  0.039   0.141   1430
  Planarity :  0.004   0.031   1490
  Dihedral  : 13.224 168.985   1896
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.56 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.26), residues: 1076
  helix:  0.71 (0.22), residues: 624
  sheet: -1.40 (0.57), residues: 74
  loop : -2.47 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 345 
 TYR   0.006   0.001   TYR B 510 
 PHE   0.018   0.001   PHE A 281 
 TRP   0.007   0.001   TRP A 583 
 HIS   0.006   0.001   HIS B 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9146)
  covalent geometry    : angle       0.57507 (12408)
  SS BOND              : bond        0.00705 (    2)
  SS BOND              : angle       1.28686 (    4)
  hydrogen bonds       : bond        0.03334 (  454)
  hydrogen bonds       : angle       4.03329 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  171 HIS cc_start: 0.8202 (m-70) cc_final: 0.7947 (m90)
REVERT: A  178 MET cc_start: 0.7977 (mmm) cc_final: 0.7439 (mmm)
REVERT: A  404 ILE cc_start: 0.7968 (tt) cc_final: 0.7671 (mt)
REVERT: A  407 ASP cc_start: 0.8501 (t0) cc_final: 0.8066 (m-30)
REVERT: A  492 MET cc_start: 0.7606 (mmm) cc_final: 0.7161 (mtp)
REVERT: A  511 TRP cc_start: 0.7913 (m100) cc_final: 0.7511 (m-10)
REVERT: B  171 HIS cc_start: 0.8160 (m-70) cc_final: 0.7888 (m90)
REVERT: B  178 MET cc_start: 0.7923 (mmm) cc_final: 0.7301 (mmm)
REVERT: B  179 MET cc_start: 0.8606 (tpp) cc_final: 0.8239 (tpt)
REVERT: B  277 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7915 (p)
REVERT: B  404 ILE cc_start: 0.7981 (tt) cc_final: 0.7686 (mt)
REVERT: B  407 ASP cc_start: 0.8470 (t0) cc_final: 0.8015 (m-30)
REVERT: B  492 MET cc_start: 0.7689 (mmm) cc_final: 0.7268 (mtp)
REVERT: B  511 TRP cc_start: 0.7885 (m100) cc_final: 0.7456 (m-10)
REVERT: B  609 LEU cc_start: 0.8156 (tp) cc_final: 0.7945 (tp)
  outliers start: 26
  outliers final: 17
  residues processed: 165
  average time/residue: 0.0717
  time to fit residues: 17.4471
Evaluate side-chains
  152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
B 418 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.132076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.115782 restraints weight = 12929.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.118020 restraints weight = 8492.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.119735 restraints weight = 6188.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.120818 restraints weight = 4856.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.121693 restraints weight = 4047.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9148  Z= 0.223
  Angle     :  0.671   6.078  12412  Z= 0.327
  Chirality :  0.043   0.146   1430
  Planarity :  0.004   0.034   1490
  Dihedral  : 12.997 171.815   1896
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.31 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.26), residues: 1076
  helix:  0.49 (0.21), residues: 634
  sheet: -1.62 (0.56), residues: 74
  loop : -2.69 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 298 
 TYR   0.027   0.002   TYR B 297 
 PHE   0.010   0.002   PHE A 239 
 TRP   0.003   0.001   TRP B 583 
 HIS   0.013   0.002   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 9146)
  covalent geometry    : angle       0.67110 (12408)
  SS BOND              : bond        0.00546 (    2)
  SS BOND              : angle       1.37633 (    4)
  hydrogen bonds       : bond        0.03934 (  454)
  hydrogen bonds       : angle       4.21229 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  178 MET cc_start: 0.7983 (mmm) cc_final: 0.7593 (mmm)
REVERT: A  404 ILE cc_start: 0.8050 (tt) cc_final: 0.7764 (mt)
REVERT: A  407 ASP cc_start: 0.8479 (t0) cc_final: 0.8224 (m-30)
REVERT: A  492 MET cc_start: 0.7726 (mmm) cc_final: 0.7321 (mtp)
REVERT: A  511 TRP cc_start: 0.8071 (m100) cc_final: 0.7620 (m-10)
REVERT: B  178 MET cc_start: 0.8034 (mmm) cc_final: 0.7378 (mmm)
REVERT: B  179 MET cc_start: 0.8593 (tpp) cc_final: 0.8104 (tpt)
REVERT: B  404 ILE cc_start: 0.8056 (tt) cc_final: 0.7775 (mt)
REVERT: B  407 ASP cc_start: 0.8449 (t0) cc_final: 0.8190 (m-30)
REVERT: B  492 MET cc_start: 0.7741 (mmm) cc_final: 0.7300 (mtp)
REVERT: B  511 TRP cc_start: 0.8053 (m100) cc_final: 0.7626 (m-10)
REVERT: B  609 LEU cc_start: 0.8253 (tp) cc_final: 0.8020 (tp)
  outliers start: 28
  outliers final: 24
  residues processed: 153
  average time/residue: 0.0679
  time to fit residues: 15.6456
Evaluate side-chains
  149 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  625 ILE
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  517 SER
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  625 ILE
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 418 HIS
B 418 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.135538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.119246 restraints weight = 12700.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.121631 restraints weight = 8281.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.123340 restraints weight = 5997.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124583 restraints weight = 4666.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.125412 restraints weight = 3830.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9148  Z= 0.121
  Angle     :  0.590   8.414  12412  Z= 0.284
  Chirality :  0.039   0.138   1430
  Planarity :  0.004   0.034   1490
  Dihedral  : 12.478 168.070   1896
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.39 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.26), residues: 1076
  helix:  0.71 (0.21), residues: 636
  sheet: -1.45 (0.56), residues: 74
  loop : -2.60 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.016   0.001   TYR B 297 
 PHE   0.008   0.001   PHE B 281 
 TRP   0.007   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9146)
  covalent geometry    : angle       0.58910 (12408)
  SS BOND              : bond        0.00703 (    2)
  SS BOND              : angle       1.46305 (    4)
  hydrogen bonds       : bond        0.03465 (  454)
  hydrogen bonds       : angle       3.99788 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  139 MET cc_start: 0.6936 (ppp) cc_final: 0.6563 (ptt)
REVERT: A  178 MET cc_start: 0.7948 (mmm) cc_final: 0.7510 (mmm)
REVERT: A  404 ILE cc_start: 0.7980 (tt) cc_final: 0.7758 (mt)
REVERT: A  405 MET cc_start: 0.8312 (tmm) cc_final: 0.7853 (tmm)
REVERT: A  492 MET cc_start: 0.7659 (mmm) cc_final: 0.7308 (mtp)
REVERT: A  500 MET cc_start: 0.7055 (mmt) cc_final: 0.6390 (mtm)
REVERT: A  511 TRP cc_start: 0.7938 (m100) cc_final: 0.7498 (m-10)
REVERT: B  179 MET cc_start: 0.8613 (tpp) cc_final: 0.8202 (tpt)
REVERT: B  404 ILE cc_start: 0.7979 (tt) cc_final: 0.7762 (mt)
REVERT: B  405 MET cc_start: 0.8338 (tmm) cc_final: 0.7872 (tmm)
REVERT: B  492 MET cc_start: 0.7663 (mmm) cc_final: 0.7263 (mtp)
REVERT: B  500 MET cc_start: 0.6983 (mmt) cc_final: 0.6362 (mtm)
REVERT: B  511 TRP cc_start: 0.7910 (m100) cc_final: 0.7504 (m-10)
  outliers start: 24
  outliers final: 18
  residues processed: 155
  average time/residue: 0.0639
  time to fit residues: 15.0206
Evaluate side-chains
  150 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
B 418 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.137640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.121061 restraints weight = 12668.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.123477 restraints weight = 7994.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.125325 restraints weight = 5679.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.126581 restraints weight = 4360.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.127427 restraints weight = 3550.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9148  Z= 0.124
  Angle     :  0.593   9.146  12412  Z= 0.286
  Chirality :  0.040   0.160   1430
  Planarity :  0.004   0.035   1490
  Dihedral  : 12.270 165.211   1896
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.28 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.26), residues: 1076
  helix:  0.88 (0.21), residues: 640
  sheet: -1.43 (0.57), residues: 74
  loop : -2.75 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.012   0.001   TYR B 297 
 PHE   0.011   0.001   PHE A 281 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.009   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9146)
  covalent geometry    : angle       0.59302 (12408)
  SS BOND              : bond        0.00664 (    2)
  SS BOND              : angle       1.33926 (    4)
  hydrogen bonds       : bond        0.03402 (  454)
  hydrogen bonds       : angle       3.97566 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  178 MET cc_start: 0.7986 (mmm) cc_final: 0.7316 (mmm)
REVERT: A  405 MET cc_start: 0.8270 (tmm) cc_final: 0.7832 (tmm)
REVERT: A  407 ASP cc_start: 0.8543 (t0) cc_final: 0.8201 (m-30)
REVERT: A  492 MET cc_start: 0.7651 (mmm) cc_final: 0.7297 (mtp)
REVERT: A  500 MET cc_start: 0.7031 (mmt) cc_final: 0.6377 (mtm)
REVERT: A  511 TRP cc_start: 0.7951 (m100) cc_final: 0.7485 (m-10)
REVERT: A  660 TYR cc_start: 0.7971 (t80) cc_final: 0.7551 (t80)
REVERT: B  178 MET cc_start: 0.7909 (mmm) cc_final: 0.7341 (mmm)
REVERT: B  179 MET cc_start: 0.8625 (tpp) cc_final: 0.8318 (tpt)
REVERT: B  405 MET cc_start: 0.8303 (tmm) cc_final: 0.7853 (tmm)
REVERT: B  407 ASP cc_start: 0.8519 (t0) cc_final: 0.8172 (m-30)
REVERT: B  492 MET cc_start: 0.7651 (mmm) cc_final: 0.7249 (mtp)
REVERT: B  500 MET cc_start: 0.6952 (mmt) cc_final: 0.6322 (mtm)
REVERT: B  511 TRP cc_start: 0.7915 (m100) cc_final: 0.7472 (m-10)
REVERT: B  660 TYR cc_start: 0.7938 (t80) cc_final: 0.7526 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 160
  average time/residue: 0.0672
  time to fit residues: 16.2295
Evaluate side-chains
  152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  517 SER
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 102 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 418 HIS
B 171 HIS
B 418 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.137988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.121189 restraints weight = 12579.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.123692 restraints weight = 8002.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125533 restraints weight = 5678.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.126703 restraints weight = 4387.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.127680 restraints weight = 3603.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9148  Z= 0.127
  Angle     :  0.592   7.899  12412  Z= 0.286
  Chirality :  0.041   0.243   1430
  Planarity :  0.004   0.035   1490
  Dihedral  : 12.151 159.656   1896
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.39 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.26), residues: 1076
  helix:  0.91 (0.21), residues: 644
  sheet: -1.39 (0.58), residues: 74
  loop : -2.66 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 414 
 TYR   0.010   0.001   TYR B 297 
 PHE   0.013   0.001   PHE B 281 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.009   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9146)
  covalent geometry    : angle       0.59186 (12408)
  SS BOND              : bond        0.00662 (    2)
  SS BOND              : angle       1.29896 (    4)
  hydrogen bonds       : bond        0.03342 (  454)
  hydrogen bonds       : angle       3.95453 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8024 (mmm) cc_final: 0.7345 (mmm)
REVERT: A  405 MET cc_start: 0.8424 (tmm) cc_final: 0.7888 (tmm)
REVERT: A  407 ASP cc_start: 0.8429 (t0) cc_final: 0.8107 (m-30)
REVERT: A  492 MET cc_start: 0.7646 (mmm) cc_final: 0.7296 (mtp)
REVERT: A  500 MET cc_start: 0.6997 (mmt) cc_final: 0.6384 (mtm)
REVERT: A  511 TRP cc_start: 0.7914 (m100) cc_final: 0.7426 (m-10)
REVERT: A  660 TYR cc_start: 0.7952 (t80) cc_final: 0.7537 (t80)
REVERT: B  178 MET cc_start: 0.7960 (mmm) cc_final: 0.7400 (mmm)
REVERT: B  179 MET cc_start: 0.8625 (tpp) cc_final: 0.8306 (tpt)
REVERT: B  405 MET cc_start: 0.8459 (tmm) cc_final: 0.7905 (tmm)
REVERT: B  407 ASP cc_start: 0.8396 (t0) cc_final: 0.8086 (m-30)
REVERT: B  492 MET cc_start: 0.7656 (mmm) cc_final: 0.7268 (mtp)
REVERT: B  500 MET cc_start: 0.6967 (mmt) cc_final: 0.6324 (mtm)
REVERT: B  511 TRP cc_start: 0.7905 (m100) cc_final: 0.7439 (m-10)
REVERT: B  660 TYR cc_start: 0.7940 (t80) cc_final: 0.7532 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 160
  average time/residue: 0.0672
  time to fit residues: 16.3614
Evaluate side-chains
  158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  517 SER
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 67 optimal weight:    0.0000
   chunk 69 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0030
   chunk 27 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 34 optimal weight:    0.4980
   chunk 1 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 418 HIS
A 618 HIS
B 171 HIS
B 418 HIS
B 618 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.139221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.123062 restraints weight = 12408.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.125464 restraints weight = 8034.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.127234 restraints weight = 5766.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.128406 restraints weight = 4452.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.129323 restraints weight = 3657.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9148  Z= 0.102
  Angle     :  0.567   6.616  12412  Z= 0.275
  Chirality :  0.038   0.133   1430
  Planarity :  0.003   0.036   1490
  Dihedral  : 11.903 151.960   1896
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.46 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1076
  helix:  1.13 (0.22), residues: 638
  sheet: -1.29 (0.58), residues: 74
  loop : -2.64 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 606 
 TYR   0.010   0.001   TYR A 297 
 PHE   0.015   0.001   PHE B 501 
 TRP   0.009   0.001   TRP B 583 
 HIS   0.005   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 9146)
  covalent geometry    : angle       0.56708 (12408)
  SS BOND              : bond        0.00709 (    2)
  SS BOND              : angle       1.24720 (    4)
  hydrogen bonds       : bond        0.03123 (  454)
  hydrogen bonds       : angle       3.84174 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8045 (mmm) cc_final: 0.7435 (mmm)
REVERT: A  275 GLN cc_start: 0.7843 (mt0) cc_final: 0.7636 (tp40)
REVERT: A  405 MET cc_start: 0.8396 (tmm) cc_final: 0.7941 (tmm)
REVERT: A  492 MET cc_start: 0.7624 (mmm) cc_final: 0.7258 (mtp)
REVERT: A  500 MET cc_start: 0.6882 (mmt) cc_final: 0.6415 (mtm)
REVERT: A  511 TRP cc_start: 0.7814 (m100) cc_final: 0.7406 (m-10)
REVERT: A  660 TYR cc_start: 0.7909 (t80) cc_final: 0.7515 (t80)
REVERT: B  178 MET cc_start: 0.7962 (mmm) cc_final: 0.7408 (mmm)
REVERT: B  179 MET cc_start: 0.8592 (tpp) cc_final: 0.8294 (tpt)
REVERT: B  405 MET cc_start: 0.8435 (tmm) cc_final: 0.7967 (tmm)
REVERT: B  492 MET cc_start: 0.7648 (mmm) cc_final: 0.7263 (mtp)
REVERT: B  500 MET cc_start: 0.6818 (mmt) cc_final: 0.6392 (mtm)
REVERT: B  511 TRP cc_start: 0.7755 (m100) cc_final: 0.7384 (m-10)
REVERT: B  660 TYR cc_start: 0.7891 (t80) cc_final: 0.7499 (t80)
  outliers start: 19
  outliers final: 18
  residues processed: 168
  average time/residue: 0.0633
  time to fit residues: 16.1224
Evaluate side-chains
  155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  517 SER
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 86 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 320 ASN
A 418 HIS
B 320 ASN
B 418 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.138845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.123009 restraints weight = 12468.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.125357 restraints weight = 8025.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127059 restraints weight = 5726.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.128128 restraints weight = 4408.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.129062 restraints weight = 3652.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9148  Z= 0.178
  Angle     :  0.620   6.306  12412  Z= 0.305
  Chirality :  0.041   0.139   1430
  Planarity :  0.004   0.037   1490
  Dihedral  : 12.021 149.602   1896
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 21.57 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.26), residues: 1076
  helix:  1.00 (0.21), residues: 640
  sheet: -1.41 (0.58), residues: 74
  loop : -2.61 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 224 
 TYR   0.009   0.001   TYR B 288 
 PHE   0.011   0.002   PHE B 501 
 TRP   0.003   0.001   TRP B 583 
 HIS   0.005   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 9146)
  covalent geometry    : angle       0.61945 (12408)
  SS BOND              : bond        0.00487 (    2)
  SS BOND              : angle       1.08127 (    4)
  hydrogen bonds       : bond        0.03551 (  454)
  hydrogen bonds       : angle       3.96716 ( 1338)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  405 MET cc_start: 0.8465 (tmm) cc_final: 0.7969 (tmm)
REVERT: A  407 ASP cc_start: 0.8344 (t0) cc_final: 0.8045 (m-30)
REVERT: A  492 MET cc_start: 0.7658 (mmm) cc_final: 0.7292 (mtp)
REVERT: A  500 MET cc_start: 0.6950 (mmt) cc_final: 0.6422 (mtm)
REVERT: A  511 TRP cc_start: 0.8078 (m100) cc_final: 0.7563 (m-10)
REVERT: B  117 MET cc_start: 0.7804 (mtt) cc_final: 0.7596 (mtt)
REVERT: B  179 MET cc_start: 0.8586 (tpp) cc_final: 0.8158 (tpt)
REVERT: B  405 MET cc_start: 0.8485 (tmm) cc_final: 0.7990 (tmm)
REVERT: B  407 ASP cc_start: 0.8333 (t0) cc_final: 0.8062 (m-30)
REVERT: B  492 MET cc_start: 0.7708 (mmm) cc_final: 0.7318 (mtp)
REVERT: B  511 TRP cc_start: 0.8023 (m100) cc_final: 0.7532 (m-10)
REVERT: B  660 TYR cc_start: 0.7977 (t80) cc_final: 0.7570 (t80)
  outliers start: 23
  outliers final: 20
  residues processed: 153
  average time/residue: 0.0632
  time to fit residues: 14.7138
Evaluate side-chains
  152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  160 CYS
Chi-restraints excluded: chain B residue  320 ASN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  517 SER
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0020
   chunk 8 optimal weight:    0.0870
   chunk 65 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5570

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
B 320 ASN
B 418 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.137955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122056 restraints weight = 12346.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124396 restraints weight = 7929.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.126186 restraints weight = 5665.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127460 restraints weight = 4364.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128137 restraints weight = 3542.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9148  Z= 0.112
  Angle     :  0.580   7.806  12412  Z= 0.284
  Chirality :  0.040   0.265   1430
  Planarity :  0.004   0.036   1490
  Dihedral  : 11.850 144.684   1896
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 22.32 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.26), residues: 1076
  helix:  1.05 (0.21), residues: 642
  sheet: -1.24 (0.58), residues: 74
  loop : -2.53 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 156 
 TYR   0.010   0.001   TYR B 297 
 PHE   0.008   0.001   PHE B 281 
 TRP   0.010   0.002   TRP A 583 
 HIS   0.007   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9146)
  covalent geometry    : angle       0.57973 (12408)
  SS BOND              : bond        0.00671 (    2)
  SS BOND              : angle       1.28898 (    4)
  hydrogen bonds       : bond        0.03280 (  454)
  hydrogen bonds       : angle       3.85174 ( 1338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1320.40 seconds
wall clock time: 23 minutes 36.24 seconds (1416.24 seconds total)