Starting phenix.real_space_refine
on Mon Apr 28 15:02:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nph_0470/04_2025/6nph_0470.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nph_0470/04_2025/6nph_0470.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nph_0470/04_2025/6nph_0470.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nph_0470/04_2025/6nph_0470.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nph_0470/04_2025/6nph_0470.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nph_0470/04_2025/6nph_0470.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.013
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: 7
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     P       7      5.49       5
     S      46      5.16       5
     Cl      4      4.86       5
     C    5016      2.51       5
     N    1119      2.21       5
     O    1310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7504
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3567
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 13, 'TRANS': 458}
    Chain: "B"
      Number of atoms: 3567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3567
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 13, 'TRANS': 458}
    Chain: "A"
      Number of atoms: 159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 159
          Unusual residues: {'  K': 1, ' CL': 2, 'POV': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 211
          Unusual residues: {'  K': 1, ' CL': 2, 'POV': 4}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 4.91, per 1000 atoms: 0.65
  Number of scatterers: 7504
  At special positions: 0
  Unit cell: (105.5, 77.015, 90.73, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     K       2     19.00
     Cl      4     17.00
     S      46     16.00
     P       7     15.00
     O    1310      8.00
     N    1119      7.00
     C    5016      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 496 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 496 " - pdb=" SG  CYS B 507 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.76
  Conformation dependent library (CDL) restraints added in 972.2 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      70.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 213 through 222
    Processing helix  chain 'A' and resid 230 through 237
    Processing helix  chain 'A' and resid 238 through 265
    Processing helix  chain 'A' and resid 273 through 282
      removed outlier: 3.973A  pdb=" N   LEU A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 320
      removed outlier: 3.741A  pdb=" N   SER A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ALA A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET A 304 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 341
      removed outlier: 3.580A  pdb=" N   ILE A 331 " --> pdb=" O   GLN A 327 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 332 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 349
    Processing helix  chain 'A' and resid 349 through 375
      removed outlier: 3.919A  pdb=" N   GLU A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ALA A 354 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LYS A 355 " --> pdb=" O   GLU A 351 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN A 357 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   ILE A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   PHE A 359 " --> pdb=" O   LYS A 355 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR A 366 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 398
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 419
      No H-bonds generated for 'chain 'A' and resid 417 through 419'
    Processing helix  chain 'A' and resid 421 through 425
      removed outlier: 3.552A  pdb=" N   ALA A 424 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLY A 425 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 421 through 425'
    Processing helix  chain 'A' and resid 434 through 463
      Proline residue:  A 440  - end of helix
      removed outlier: 3.691A  pdb=" N   LEU A 444 " --> pdb=" O   PRO A 440 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 522
    Processing helix  chain 'A' and resid 527 through 530
    Processing helix  chain 'A' and resid 531 through 545
    Processing helix  chain 'A' and resid 546 through 555
    Processing helix  chain 'A' and resid 561 through 566
      removed outlier: 4.178A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ILE A 565 " --> pdb=" O   GLY A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 592
      removed outlier: 3.572A  pdb=" N   PHE A 590 " --> pdb=" O   ILE A 586 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU A 592 " --> pdb=" O   LEU A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 625
      Proline residue:  A 601  - end of helix
      removed outlier: 3.511A  pdb=" N   ASN A 625 " --> pdb=" O   ALA A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 656
      removed outlier: 3.587A  pdb=" N   ASN A 656 " --> pdb=" O   MET A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 676
      removed outlier: 3.646A  pdb=" N   VAL A 674 " --> pdb=" O   LEU A 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 213
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 238 through 265
    Processing helix  chain 'B' and resid 273 through 282
      removed outlier: 3.973A  pdb=" N   LEU B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 320
      removed outlier: 3.743A  pdb=" N   SER B 289 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ALA B 303 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET B 304 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B 320 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 341
      removed outlier: 3.581A  pdb=" N   ILE B 331 " --> pdb=" O   GLN B 327 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG B 332 " --> pdb=" O   THR B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 349
    Processing helix  chain 'B' and resid 349 through 375
      removed outlier: 3.920A  pdb=" N   GLU B 353 " --> pdb=" O   GLY B 349 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ALA B 354 " --> pdb=" O   MET B 350 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LYS B 355 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN B 357 " --> pdb=" O   GLU B 353 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   ILE B 358 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   PHE B 359 " --> pdb=" O   LYS B 355 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   THR B 366 " --> pdb=" O   VAL B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 398
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 419
      No H-bonds generated for 'chain 'B' and resid 417 through 419'
    Processing helix  chain 'B' and resid 421 through 425
      removed outlier: 3.551A  pdb=" N   ALA B 424 " --> pdb=" O   GLY B 421 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLY B 425 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 421 through 425'
    Processing helix  chain 'B' and resid 434 through 463
      Proline residue:  B 440  - end of helix
      removed outlier: 3.692A  pdb=" N   LEU B 444 " --> pdb=" O   PRO B 440 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 522
    Processing helix  chain 'B' and resid 527 through 530
    Processing helix  chain 'B' and resid 531 through 545
    Processing helix  chain 'B' and resid 546 through 555
    Processing helix  chain 'B' and resid 561 through 566
      removed outlier: 4.177A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 561 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ILE B 565 " --> pdb=" O   GLY B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 592
      removed outlier: 3.573A  pdb=" N   PHE B 590 " --> pdb=" O   ILE B 586 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B 592 " --> pdb=" O   LEU B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 625
      Proline residue:  B 601  - end of helix
      removed outlier: 3.511A  pdb=" N   ASN B 625 " --> pdb=" O   ALA B 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 656
      removed outlier: 3.587A  pdb=" N   ASN B 656 " --> pdb=" O   MET B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 676
      removed outlier: 3.645A  pdb=" N   VAL B 674 " --> pdb=" O   LEU B 670 " (cutoff:3.500A)

    428 hydrogen bonds defined for protein.
    1272 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: 1.85

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1108
        1.31 -     1.43: 2113
        1.43 -     1.56: 4241
        1.56 -     1.69: 124
        1.69 -     1.82: 77
  Bond restraints: 7663
  Sorted by residual:
  bond pdb=" C31 POV A 702 "
       pdb=" O31 POV A 702 "
    ideal  model  delta    sigma   weight residual
    1.327  1.438 -0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" C31 POV A 701 "
       pdb=" O31 POV A 701 "
    ideal  model  delta    sigma   weight residual
    1.327  1.436 -0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C31 POV B 802 "
       pdb=" O31 POV B 802 "
    ideal  model  delta    sigma   weight residual
    1.327  1.432 -0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" C31 POV B 801 "
       pdb=" O31 POV B 801 "
    ideal  model  delta    sigma   weight residual
    1.327  1.431 -0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" C21 POV A 703 "
       pdb=" O21 POV A 703 "
    ideal  model  delta    sigma   weight residual
    1.330  1.433 -0.103 2.00e-02 2.50e+03 2.66e+01
  ... (remaining 7658 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.22: 10278
        6.22 -    12.44: 65
       12.44 -    18.67: 2
       18.67 -    24.89: 2
       24.89 -    31.11: 4
  Bond angle restraints: 10351
  Sorted by residual:
  angle pdb=" C12 POV A 703 "
        pdb=" N   POV A 703 "
        pdb=" C15 POV A 703 "
      ideal   model   delta    sigma   weight residual
     112.10   80.99   31.11 3.00e+00 1.11e-01 1.08e+02
  angle pdb=" C13 POV A 703 "
        pdb=" N   POV A 703 "
        pdb=" C14 POV A 703 "
      ideal   model   delta    sigma   weight residual
     108.80   79.67   29.13 3.00e+00 1.11e-01 9.43e+01
  angle pdb=" C13 POV A 703 "
        pdb=" N   POV A 703 "
        pdb=" C15 POV A 703 "
      ideal   model   delta    sigma   weight residual
     109.35   80.29   29.06 3.00e+00 1.11e-01 9.38e+01
  angle pdb=" C12 POV A 703 "
        pdb=" N   POV A 703 "
        pdb=" C14 POV A 703 "
      ideal   model   delta    sigma   weight residual
     107.13   80.42   26.71 3.00e+00 1.11e-01 7.93e+01
  angle pdb=" C14 POV A 703 "
        pdb=" N   POV A 703 "
        pdb=" C15 POV A 703 "
      ideal   model   delta    sigma   weight residual
     108.02  132.52  -24.50 3.00e+00 1.11e-01 6.67e+01
  ... (remaining 10346 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.94: 4223
       28.94 -    57.87: 210
       57.87 -    86.81: 34
       86.81 -   115.75: 5
      115.75 -   144.68: 5
  Dihedral angle restraints: 4477
    sinusoidal: 1791
      harmonic: 2686
  Sorted by residual:
  dihedral pdb=" CD  ARG A 630 "
           pdb=" NE  ARG A 630 "
           pdb=" CZ  ARG A 630 "
           pdb=" NH1 ARG A 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -41.33   41.33     1      1.00e+01 1.00e-02 2.39e+01
  dihedral pdb=" CA  ALA A 530 "
           pdb=" C   ALA A 530 "
           pdb=" N   GLY A 531 "
           pdb=" CA  GLY A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.86   24.14     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ALA B 530 "
           pdb=" C   ALA B 530 "
           pdb=" N   GLY B 531 "
           pdb=" CA  GLY B 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.88   24.12     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 4474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 667
       0.043 -    0.085: 360
       0.085 -    0.128: 110
       0.128 -    0.170: 33
       0.170 -    0.213: 7
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" CA  PHE B 387 "
            pdb=" N   PHE B 387 "
            pdb=" C   PHE B 387 "
            pdb=" CB  PHE B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  PHE A 387 "
            pdb=" N   PHE A 387 "
            pdb=" C   PHE A 387 "
            pdb=" CB  PHE A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  SER A 525 "
            pdb=" N   SER A 525 "
            pdb=" C   SER A 525 "
            pdb=" CB  SER A 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1174 not shown)

  Planarity restraints: 1243
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 630 "    0.719 9.50e-02 1.11e+02   3.22e-01 6.33e+01
        pdb=" NE  ARG A 630 "   -0.043 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 630 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 630 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 630 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 630 "   -0.309 9.50e-02 1.11e+02   1.39e-01 1.18e+01
        pdb=" NE  ARG B 630 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 630 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 630 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 630 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 416 "    0.047 5.00e-02 4.00e+02   6.94e-02 7.70e+00
        pdb=" N   PRO B 417 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 417 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 417 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1240 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.86: 2663
        2.86 -     3.43: 7669
        3.43 -     4.00: 13623
        4.00 -     4.57: 20248
        4.57 -     5.14: 29229
  Nonbonded interactions: 73432
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 474 "
            pdb=" O   GLY B 490 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER A 474 "
            pdb=" O   GLY A 490 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   MET A 518 "
            pdb=" OG  SER A 522 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   MET B 518 "
            pdb=" OG  SER B 522 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OE1 GLN B 406 "
            pdb=" OG  SER B 410 "
     model   vdw
     2.322 3.040
  ... (remaining 73427 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 206 through 677 or resid 701 through 703 or resid 706))
  selection = (chain 'B' and (resid 206 through 677 or resid 801 through 803 or resid 806))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.040
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
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      :  0.012   0.111   7665  Z= 0.568
  Angle     :  1.415  31.111  10355  Z= 0.626
  Chirality :  0.058   0.213   1177
  Planarity :  0.012   0.322   1243
  Dihedral  : 18.336 144.683   2763
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  :  7.73 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.29 (0.20), residues: 940
  helix: -2.32 (0.15), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.64 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 657 
 HIS   0.003   0.001   HIS A 512 
 PHE   0.032   0.003   PHE B 387 
 TYR   0.010   0.002   TYR B 491 
 ARG   0.004   0.001   ARG B 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17575 (  428)
  hydrogen bonds       : angle       6.57054 ( 1272)
  SS BOND              : bond        0.00493 (    2)
  SS BOND              : angle       0.74530 (    4)
  covalent geometry    : bond        0.01220 ( 7663)
  covalent geometry    : angle       1.41548 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 181
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A  525 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7876 (p)
REVERT: A  568 LYS cc_start: 0.6795 (tttt) cc_final: 0.6162 (tmtm)
REVERT: B  211 LYS cc_start: 0.7463 (tttm) cc_final: 0.6281 (mptt)
REVERT: B  575 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7341 (pt0)
  outliers start: 35
  outliers final: 6
  residues processed: 213
  average time/residue: 0.8916
  time to fit residues: 204.2265
Evaluate side-chains
  121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  557 ASP
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  557 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0010
   chunk 44 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
A 298 ASN
A 327 GLN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN
A 664 ASN
B 298 ASN
B 327 GLN
B 357 GLN
B 512 HIS
B 664 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.143116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.113520 restraints weight = 8452.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.84
r_work: 0.3191 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7665  Z= 0.137
  Angle     :  0.620  12.977  10355  Z= 0.315
  Chirality :  0.043   0.161   1177
  Planarity :  0.004   0.054   1243
  Dihedral  : 16.533 105.556   1309
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 15.20 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.26), residues: 940
  helix: -0.08 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop : -3.22 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 209 
 HIS   0.003   0.001   HIS A 620 
 PHE   0.015   0.001   PHE A 415 
 TYR   0.015   0.001   TYR A 371 
 ARG   0.004   0.001   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  428)
  hydrogen bonds       : angle       3.96349 ( 1272)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.87128 (    4)
  covalent geometry    : bond        0.00296 ( 7663)
  covalent geometry    : angle       0.61982 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  568 LYS cc_start: 0.7616 (tttt) cc_final: 0.6762 (tttm)
REVERT: A  634 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8139 (ttmt)
REVERT: B  304 MET cc_start: 0.9022 (ttp) cc_final: 0.8697 (ttp)
REVERT: B  345 ILE cc_start: 0.8532 (mt) cc_final: 0.8262 (mp)
REVERT: B  364 LEU cc_start: 0.7676 (tp) cc_final: 0.7416 (tt)
REVERT: B  373 ILE cc_start: 0.8438 (pt) cc_final: 0.7941 (mt)
REVERT: B  479 ILE cc_start: 0.5618 (OUTLIER) cc_final: 0.5092 (mm)
REVERT: B  524 PHE cc_start: 0.8019 (t80) cc_final: 0.7183 (t80)
REVERT: B  549 LYS cc_start: 0.8149 (tptm) cc_final: 0.7732 (tppt)
REVERT: B  575 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7494 (pt0)
  outliers start: 41
  outliers final: 11
  residues processed: 157
  average time/residue: 1.0111
  time to fit residues: 170.7918
Evaluate side-chains
  122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  507 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0870
   chunk 79 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 427 ASN
A 436 GLN
B 512 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.138578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.108579 restraints weight = 8580.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.92
r_work: 0.3124 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.5817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7665  Z= 0.109
  Angle     :  0.526   8.293  10355  Z= 0.274
  Chirality :  0.041   0.167   1177
  Planarity :  0.003   0.042   1243
  Dihedral  : 15.870 107.829   1301
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.60 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.27), residues: 940
  helix:  1.03 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.09 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 209 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.015   0.001   PHE A 387 
 TYR   0.009   0.001   TYR B 570 
 ARG   0.002   0.000   ARG B 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03852 (  428)
  hydrogen bonds       : angle       3.55979 ( 1272)
  SS BOND              : bond        0.00411 (    2)
  SS BOND              : angle       0.52486 (    4)
  covalent geometry    : bond        0.00231 ( 7663)
  covalent geometry    : angle       0.52601 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 1.272 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8078 (pm20) cc_final: 0.7824 (pm20)
REVERT: A  340 ILE cc_start: 0.8393 (pp) cc_final: 0.8176 (pt)
REVERT: A  381 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8145 (t)
REVERT: A  568 LYS cc_start: 0.7692 (tttt) cc_final: 0.7057 (tttm)
REVERT: A  570 TYR cc_start: 0.7960 (m-80) cc_final: 0.7585 (m-80)
REVERT: B  304 MET cc_start: 0.9078 (ttp) cc_final: 0.8827 (ttp)
REVERT: B  315 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6179 (mt-10)
REVERT: B  345 ILE cc_start: 0.8318 (mt) cc_final: 0.7997 (mm)
REVERT: B  373 ILE cc_start: 0.8528 (pt) cc_final: 0.8078 (mt)
REVERT: B  377 ILE cc_start: 0.9133 (mt) cc_final: 0.8849 (mp)
REVERT: B  494 SER cc_start: 0.7331 (t) cc_final: 0.6931 (m)
REVERT: B  575 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7483 (pt0)
  outliers start: 24
  outliers final: 8
  residues processed: 142
  average time/residue: 1.3312
  time to fit residues: 207.6770
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  534 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 27 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   chunk 73 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
B 512 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.108228 restraints weight = 8590.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.88
r_work: 0.2976 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.6834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7665  Z= 0.104
  Angle     :  0.508   6.892  10355  Z= 0.263
  Chirality :  0.041   0.166   1177
  Planarity :  0.003   0.037   1243
  Dihedral  : 14.954 106.782   1301
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 20.93 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.28), residues: 940
  helix:  1.51 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -2.92 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 209 
 HIS   0.002   0.001   HIS A 512 
 PHE   0.013   0.001   PHE B 415 
 TYR   0.009   0.001   TYR B 676 
 ARG   0.003   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  428)
  hydrogen bonds       : angle       3.46249 ( 1272)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.10438 (    4)
  covalent geometry    : bond        0.00229 ( 7663)
  covalent geometry    : angle       0.50795 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8166 (pm20) cc_final: 0.7904 (pm20)
REVERT: A  324 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.5518 (ttt)
REVERT: A  568 LYS cc_start: 0.7961 (tttt) cc_final: 0.7233 (tttm)
REVERT: A  570 TYR cc_start: 0.8160 (m-80) cc_final: 0.7703 (m-80)
REVERT: A  577 LEU cc_start: 0.7123 (mt) cc_final: 0.6674 (mp)
REVERT: B  280 ARG cc_start: 0.7487 (mpt90) cc_final: 0.7270 (mmt-90)
REVERT: B  315 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6340 (mt-10)
REVERT: B  377 ILE cc_start: 0.9155 (mt) cc_final: 0.8900 (mp)
REVERT: B  479 ILE cc_start: 0.5542 (OUTLIER) cc_final: 0.4975 (mm)
REVERT: B  525 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7934 (t)
REVERT: B  575 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7259 (pt0)
REVERT: B  583 THR cc_start: 0.8707 (t) cc_final: 0.8427 (m)
  outliers start: 28
  outliers final: 8
  residues processed: 131
  average time/residue: 0.7138
  time to fit residues: 102.4790
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  534 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 83 optimal weight:    0.0060
   chunk 34 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
B 329 ASN
B 512 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.136023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.106644 restraints weight = 8656.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.89
r_work: 0.2904 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.7282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7665  Z= 0.102
  Angle     :  0.491   7.165  10355  Z= 0.255
  Chirality :  0.041   0.162   1177
  Planarity :  0.003   0.037   1243
  Dihedral  : 14.339 106.674   1301
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 21.33 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.28), residues: 940
  helix:  1.75 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -2.77 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 209 
 HIS   0.002   0.001   HIS B 512 
 PHE   0.013   0.001   PHE A 387 
 TYR   0.008   0.001   TYR B 676 
 ARG   0.002   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  428)
  hydrogen bonds       : angle       3.39760 ( 1272)
  SS BOND              : bond        0.00823 (    2)
  SS BOND              : angle       0.17602 (    4)
  covalent geometry    : bond        0.00221 ( 7663)
  covalent geometry    : angle       0.49073 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8125 (pm20) cc_final: 0.7829 (pm20)
REVERT: A  324 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.5702 (ttt)
REVERT: A  381 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8147 (t)
REVERT: A  568 LYS cc_start: 0.7985 (tttt) cc_final: 0.7253 (tttm)
REVERT: A  570 TYR cc_start: 0.8086 (m-80) cc_final: 0.7600 (m-80)
REVERT: A  634 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8299 (ttmt)
REVERT: B  211 LYS cc_start: 0.9049 (tttm) cc_final: 0.8791 (tttm)
REVERT: B  280 ARG cc_start: 0.7325 (mpt90) cc_final: 0.7043 (mmt-90)
REVERT: B  315 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6353 (mt-10)
REVERT: B  322 LEU cc_start: 0.7844 (mm) cc_final: 0.7531 (mm)
REVERT: B  479 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5054 (mm)
REVERT: B  494 SER cc_start: 0.7040 (t) cc_final: 0.6753 (m)
REVERT: B  575 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7194 (pt0)
REVERT: B  583 THR cc_start: 0.8614 (t) cc_final: 0.8368 (m)
  outliers start: 24
  outliers final: 8
  residues processed: 129
  average time/residue: 0.8824
  time to fit residues: 122.7736
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  534 SER
Chi-restraints excluded: chain B residue  573 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 512 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.103712 restraints weight = 8636.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.91
r_work: 0.2883 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.7552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7665  Z= 0.111
  Angle     :  0.499   7.310  10355  Z= 0.261
  Chirality :  0.041   0.162   1177
  Planarity :  0.003   0.035   1243
  Dihedral  : 14.202 106.184   1301
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.93 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 940
  helix:  1.92 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.77 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 209 
 HIS   0.003   0.001   HIS B 512 
 PHE   0.014   0.001   PHE A 387 
 TYR   0.007   0.001   TYR B 673 
 ARG   0.004   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  428)
  hydrogen bonds       : angle       3.40535 ( 1272)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.78150 (    4)
  covalent geometry    : bond        0.00249 ( 7663)
  covalent geometry    : angle       0.49926 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8285 (pm20) cc_final: 0.8023 (pm20)
REVERT: A  324 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.5760 (ttt)
REVERT: A  361 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7917 (tm)
REVERT: A  381 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8166 (t)
REVERT: A  499 THR cc_start: 0.7727 (p) cc_final: 0.7508 (m)
REVERT: A  568 LYS cc_start: 0.8055 (tttt) cc_final: 0.7304 (tttm)
REVERT: A  634 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8290 (ttmt)
REVERT: B  211 LYS cc_start: 0.9073 (tttm) cc_final: 0.8806 (tttm)
REVERT: B  225 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.6227 (mpt)
REVERT: B  280 ARG cc_start: 0.7279 (mpt90) cc_final: 0.6912 (mmt-90)
REVERT: B  315 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6400 (mt-10)
REVERT: B  322 LEU cc_start: 0.7780 (mm) cc_final: 0.7487 (mm)
REVERT: B  324 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6847 (pmm)
REVERT: B  479 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.4995 (mm)
REVERT: B  525 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8381 (p)
REVERT: B  575 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7185 (pt0)
REVERT: B  583 THR cc_start: 0.8572 (t) cc_final: 0.8324 (m)
  outliers start: 26
  outliers final: 8
  residues processed: 123
  average time/residue: 0.8455
  time to fit residues: 112.5686
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  534 SER
Chi-restraints excluded: chain B residue  573 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0020
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0770
   chunk 73 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.4546

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

Flipped N/Q/H residues before XYZ refinement:
A 436 GLN
B 512 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.138043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109216 restraints weight = 8748.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.90
r_work: 0.2929 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.7753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7665  Z= 0.092
  Angle     :  0.481   6.261  10355  Z= 0.250
  Chirality :  0.040   0.163   1177
  Planarity :  0.003   0.033   1243
  Dihedral  : 13.760 102.856   1301
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.80 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.29), residues: 940
  helix:  2.12 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.69 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 209 
 HIS   0.002   0.001   HIS A 620 
 PHE   0.013   0.001   PHE B 387 
 TYR   0.006   0.001   TYR B 570 
 ARG   0.003   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  428)
  hydrogen bonds       : angle       3.32662 ( 1272)
  SS BOND              : bond        0.00379 (    2)
  SS BOND              : angle       1.05976 (    4)
  covalent geometry    : bond        0.00190 ( 7663)
  covalent geometry    : angle       0.48023 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8271 (pm20) cc_final: 0.8011 (pm20)
REVERT: A  315 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7045 (mt-10)
REVERT: A  324 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.5725 (ttt)
REVERT: A  350 MET cc_start: 0.7674 (mmm) cc_final: 0.7008 (tpp)
REVERT: A  361 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7878 (tm)
REVERT: A  568 LYS cc_start: 0.8008 (tttt) cc_final: 0.7228 (tttm)
REVERT: A  634 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8322 (ttmt)
REVERT: B  211 LYS cc_start: 0.9051 (tttm) cc_final: 0.8792 (tttm)
REVERT: B  280 ARG cc_start: 0.7245 (mpt90) cc_final: 0.6918 (mmt-90)
REVERT: B  322 LEU cc_start: 0.7794 (mm) cc_final: 0.7500 (mm)
REVERT: B  324 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6719 (pmm)
REVERT: B  525 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8471 (p)
REVERT: B  575 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7186 (pt0)
REVERT: B  583 THR cc_start: 0.8547 (t) cc_final: 0.8307 (m)
  outliers start: 22
  outliers final: 9
  residues processed: 121
  average time/residue: 0.8475
  time to fit residues: 111.1896
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  534 SER
Chi-restraints excluded: chain B residue  573 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 48 optimal weight:    0.3980
   chunk 63 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 512 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.102338 restraints weight = 8915.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.91
r_work: 0.2872 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.7891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7665  Z= 0.152
  Angle     :  0.540   5.864  10355  Z= 0.283
  Chirality :  0.043   0.163   1177
  Planarity :  0.003   0.033   1243
  Dihedral  : 14.409 109.941   1300
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.07 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.28), residues: 940
  helix:  1.78 (0.21), residues: 630
  sheet:  None (None), residues: 0
  loop : -2.85 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 209 
 HIS   0.003   0.002   HIS B 512 
 PHE   0.018   0.002   PHE A 387 
 TYR   0.010   0.001   TYR B 673 
 ARG   0.004   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  428)
  hydrogen bonds       : angle       3.56759 ( 1272)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       1.75138 (    4)
  covalent geometry    : bond        0.00363 ( 7663)
  covalent geometry    : angle       0.53951 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8417 (pm20) cc_final: 0.8204 (pm20)
REVERT: A  315 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7293 (tt0)
REVERT: A  324 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.5876 (ttt)
REVERT: A  361 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8098 (tm)
REVERT: A  381 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8414 (t)
REVERT: A  568 LYS cc_start: 0.8177 (tttt) cc_final: 0.7455 (tttm)
REVERT: A  634 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8406 (ttmt)
REVERT: B  211 LYS cc_start: 0.9107 (tttm) cc_final: 0.8888 (tttm)
REVERT: B  225 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.6314 (mpt)
REVERT: B  280 ARG cc_start: 0.7503 (mpt90) cc_final: 0.7233 (mmt-90)
REVERT: B  322 LEU cc_start: 0.7804 (mm) cc_final: 0.7552 (mm)
REVERT: B  324 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7010 (pmm)
REVERT: B  525 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8510 (p)
REVERT: B  575 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7208 (pt0)
  outliers start: 27
  outliers final: 8
  residues processed: 107
  average time/residue: 0.9479
  time to fit residues: 108.8429
Evaluate side-chains
  96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  534 SER
Chi-restraints excluded: chain B residue  573 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 512 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.133285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104201 restraints weight = 8946.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.89
r_work: 0.2871 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.8024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7665  Z= 0.116
  Angle     :  0.518   8.567  10355  Z= 0.270
  Chirality :  0.042   0.173   1177
  Planarity :  0.003   0.033   1243
  Dihedral  : 14.008 106.445   1300
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.40 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 940
  helix:  2.01 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.69 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 209 
 HIS   0.002   0.001   HIS B 512 
 PHE   0.015   0.001   PHE B 387 
 TYR   0.007   0.001   TYR A 676 
 ARG   0.004   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  428)
  hydrogen bonds       : angle       3.44893 ( 1272)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.41662 (    4)
  covalent geometry    : bond        0.00266 ( 7663)
  covalent geometry    : angle       0.51761 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8256 (pm20) cc_final: 0.8013 (pm20)
REVERT: A  315 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7021 (mt-10)
REVERT: A  324 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.5909 (ttt)
REVERT: A  361 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7835 (tm)
REVERT: A  381 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8345 (t)
REVERT: A  518 MET cc_start: 0.8770 (mmt) cc_final: 0.8538 (mmt)
REVERT: A  572 LYS cc_start: 0.5852 (pmtt) cc_final: 0.5090 (mmtm)
REVERT: A  634 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8343 (ttmt)
REVERT: B  211 LYS cc_start: 0.9019 (tttm) cc_final: 0.8783 (tttm)
REVERT: B  280 ARG cc_start: 0.7189 (mpt90) cc_final: 0.6808 (mmt-90)
REVERT: B  322 LEU cc_start: 0.7613 (mm) cc_final: 0.7360 (mm)
REVERT: B  324 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6838 (pmm)
REVERT: B  525 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8434 (p)
  outliers start: 18
  outliers final: 6
  residues processed: 99
  average time/residue: 0.9601
  time to fit residues: 102.0329
Evaluate side-chains
  98 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  534 SER
Chi-restraints excluded: chain B residue  573 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 11 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
B 512 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.096825 restraints weight = 9026.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.97
r_work: 0.2871 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.8106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7665  Z= 0.110
  Angle     :  0.521  12.438  10355  Z= 0.267
  Chirality :  0.042   0.172   1177
  Planarity :  0.003   0.033   1243
  Dihedral  : 13.817 104.806   1300
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 22.13 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.28), residues: 940
  helix:  2.09 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.58 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 209 
 HIS   0.002   0.001   HIS A 512 
 PHE   0.014   0.001   PHE B 387 
 TYR   0.006   0.001   TYR A 676 
 ARG   0.004   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  428)
  hydrogen bonds       : angle       3.42476 ( 1272)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       1.23978 (    4)
  covalent geometry    : bond        0.00249 ( 7663)
  covalent geometry    : angle       0.52091 (10351)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8391 (pm20) cc_final: 0.8156 (pm20)
REVERT: A  315 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7157 (mt-10)
REVERT: A  361 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8027 (tm)
REVERT: A  381 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8230 (t)
REVERT: A  518 MET cc_start: 0.8842 (mmt) cc_final: 0.8609 (mmt)
REVERT: A  572 LYS cc_start: 0.5979 (pmtt) cc_final: 0.5303 (mmtm)
REVERT: A  634 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8410 (ttmt)
REVERT: B  211 LYS cc_start: 0.9103 (tttm) cc_final: 0.8871 (tttm)
REVERT: B  280 ARG cc_start: 0.7411 (mpt90) cc_final: 0.7006 (mmt-90)
REVERT: B  322 LEU cc_start: 0.7717 (mm) cc_final: 0.7468 (mm)
REVERT: B  324 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6906 (pmm)
REVERT: B  525 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8455 (p)
  outliers start: 16
  outliers final: 7
  residues processed: 101
  average time/residue: 1.1282
  time to fit residues: 122.3610
Evaluate side-chains
  101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  381 SER
Chi-restraints excluded: chain A residue  516 GLN
Chi-restraints excluded: chain A residue  525 SER
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  534 SER
Chi-restraints excluded: chain B residue  573 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.122475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.091941 restraints weight = 9042.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.96
r_work: 0.2829 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.8156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7665  Z= 0.136
  Angle     :  0.548  11.754  10355  Z= 0.283
  Chirality :  0.043   0.174   1177
  Planarity :  0.003   0.033   1243
  Dihedral  : 14.162 107.954   1300
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.40 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.28), residues: 940
  helix:  1.94 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.62 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 209 
 HIS   0.002   0.001   HIS B 512 
 PHE   0.018   0.001   PHE A 387 
 TYR   0.008   0.001   TYR B 673 
 ARG   0.004   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  428)
  hydrogen bonds       : angle       3.54364 ( 1272)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       1.25034 (    4)
  covalent geometry    : bond        0.00324 ( 7663)
  covalent geometry    : angle       0.54770 (10351)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5383.58 seconds
wall clock time: 95 minutes 34.03 seconds (5734.03 seconds total)