Starting phenix.real_space_refine
on Tue Jun 10 07:22:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byh_45031/06_2025/9byh_45031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byh_45031/06_2025/9byh_45031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byh_45031/06_2025/9byh_45031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byh_45031/06_2025/9byh_45031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byh_45031/06_2025/9byh_45031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byh_45031/06_2025/9byh_45031.cif"
  }
  resolution = 2.53
  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=   0.002 sd=   0.129
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: 6
    Type Number    sf(0)   Gaussians
     P      16      5.49       5
     Mg      2      5.21       5
     S      60      5.16       5
     C    7302      2.51       5
     N    1904      2.21       5
     O    2240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11524
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "B"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "C"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 119
          Classifications: {'peptide': 14}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
    Chain: "D"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 119
          Classifications: {'peptide': 14}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
    Chain: "A"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 89
          Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 89
          Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 8.19, per 1000 atoms: 0.71
  Number of scatterers: 11524
  At special positions: 0
  Unit cell: (91.53, 71.19, 132.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      60     16.00
     P      16     15.00
     Mg      2     11.99
     O    2240      8.00
     N    1904      7.00
     C    7302      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.11
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2660

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 11 sheets defined
      53.2% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
    Processing helix  chain 'A' and resid 25 through 39
      removed outlier: 4.096A  pdb=" N   ASP A  29 " --> pdb=" O   GLN A  25 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LYS A  30 " --> pdb=" O   PHE A  26 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 61
    Processing helix  chain 'A' and resid 65 through 71
      removed outlier: 3.987A  pdb=" N   LEU A  69 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 3.961A  pdb=" N   LYS A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 104
      removed outlier: 3.674A  pdb=" N   ALA A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 133 through 146
    Processing helix  chain 'A' and resid 152 through 159
    Processing helix  chain 'A' and resid 178 through 195
    Processing helix  chain 'A' and resid 221 through 237
      removed outlier: 4.065A  pdb=" N   GLY A 225 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   VAL A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 264
    Processing helix  chain 'A' and resid 285 through 294
      removed outlier: 3.580A  pdb=" N   VAL A 289 " --> pdb=" O   PRO A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.666A  pdb=" N   MET A 317 " --> pdb=" O   MET A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 329
      removed outlier: 5.398A  pdb=" N   ASP A 324 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   LYS A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 354
    Processing helix  chain 'A' and resid 361 through 366
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 424 through 442
    Processing helix  chain 'A' and resid 448 through 459
    Processing helix  chain 'A' and resid 467 through 475
    Processing helix  chain 'A' and resid 481 through 511
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 528 through 534
    Processing helix  chain 'A' and resid 540 through 547
    Processing helix  chain 'A' and resid 554 through 569
    Processing helix  chain 'A' and resid 583 through 588
      removed outlier: 3.622A  pdb=" N   VAL A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 646
    Processing helix  chain 'A' and resid 663 through 678
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 25 through 40
      removed outlier: 4.115A  pdb=" N   ASP B  29 " --> pdb=" O   GLN B  25 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LYS B  30 " --> pdb=" O   PHE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
    Processing helix  chain 'B' and resid 50 through 61
    Processing helix  chain 'B' and resid 65 through 71
      removed outlier: 4.052A  pdb=" N   LEU B  69 " --> pdb=" O   GLU B  65 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B  71 " --> pdb=" O   GLU B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.961A  pdb=" N   LYS B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
      removed outlier: 3.678A  pdb=" N   ALA B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 133 through 146
    Processing helix  chain 'B' and resid 152 through 159
    Processing helix  chain 'B' and resid 178 through 195
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.897A  pdb=" N   GLY B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 257 through 264
    Processing helix  chain 'B' and resid 285 through 295
      removed outlier: 3.648A  pdb=" N   VAL B 289 " --> pdb=" O   PRO B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 313 through 317
      removed outlier: 3.712A  pdb=" N   MET B 317 " --> pdb=" O   MET B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 329
      removed outlier: 6.008A  pdb=" N   ASP B 324 " --> pdb=" O   ASN B 320 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 354
    Processing helix  chain 'B' and resid 361 through 366
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 424 through 442
    Processing helix  chain 'B' and resid 448 through 459
    Processing helix  chain 'B' and resid 467 through 475
    Processing helix  chain 'B' and resid 481 through 511
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 528 through 534
    Processing helix  chain 'B' and resid 540 through 547
    Processing helix  chain 'B' and resid 554 through 569
    Processing helix  chain 'B' and resid 583 through 588
      removed outlier: 4.072A  pdb=" N   VAL B 587 " --> pdb=" O   SER B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 646
    Processing helix  chain 'B' and resid 663 through 678
    Processing helix  chain 'C' and resid 316 through 321
      removed outlier: 3.669A  pdb=" N   PHE C 320 " --> pdb=" O   ASP C 317 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TYR C 321 " --> pdb=" O   ASP C 318 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151
      removed outlier: 6.366A  pdb=" N   GLY A 412 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   MET A 466 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU A 414 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174
      removed outlier: 6.484A  pdb=" N   VAL A 199 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   TYR A 250 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU A 201 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   ASN A 252 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLY A 247 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   GLY A 281 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA A 249 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   VAL A 283 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU A 251 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301
    Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606
    Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658
      removed outlier: 6.488A  pdb=" N   LEU A 656 " --> pdb=" O   ARG A 686 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151
      removed outlier: 7.178A  pdb=" N   GLY B 462 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   ASN B 410 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLY B 464 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   GLY B 412 " --> pdb=" O   GLY B 464 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   MET B 466 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   LEU B 414 " --> pdb=" O   MET B 466 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151
      removed outlier: 4.067A  pdb=" N   CYS B 409 " --> pdb=" O   CYS B 170 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   CYS B 170 " --> pdb=" O   CYS B 409 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL B 199 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   TYR B 250 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B 201 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   ASN B 252 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLY B 247 " --> pdb=" O   SER B 279 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   GLY B 281 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ALA B 249 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   VAL B 283 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   LEU B 251 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301
    Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606
    Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659

    515 hydrogen bonds defined for protein.
    1509 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: 3.68

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3690
        1.34 -     1.46: 2772
        1.46 -     1.58: 5176
        1.58 -     1.70: 26
        1.70 -     1.81: 112
  Bond restraints: 11776
  Sorted by residual:
  bond pdb=" CB  GLU A  75 "
       pdb=" CG  GLU A  75 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.27e+00
  bond pdb=" CA  ASP A 398 "
       pdb=" CB  ASP A 398 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.017 1.69e-02 3.50e+03 1.06e+00
  bond pdb=" C5  GDP B 804 "
       pdb=" C4  GDP B 804 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.03e+00
  bond pdb=" CB  MET A 493 "
       pdb=" CG  MET A 493 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.49e-01
  bond pdb=" C5  GDP A 802 "
       pdb=" C4  GDP A 802 "
    ideal  model  delta    sigma   weight residual
    1.490  1.471  0.019 2.00e-02 2.50e+03 9.22e-01
  ... (remaining 11771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 15734
        1.92 -     3.85: 150
        3.85 -     5.77: 15
        5.77 -     7.69: 3
        7.69 -     9.62: 2
  Bond angle restraints: 15904
  Sorted by residual:
  angle pdb=" CB  MET A 493 "
        pdb=" CG  MET A 493 "
        pdb=" SD  MET A 493 "
      ideal   model   delta    sigma   weight residual
     112.70  122.32   -9.62 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" C   TYR A 397 "
        pdb=" N   ASP A 398 "
        pdb=" CA  ASP A 398 "
      ideal   model   delta    sigma   weight residual
     121.54  127.11   -5.57 1.91e+00 2.74e-01 8.50e+00
  angle pdb=" CB  MET A 595 "
        pdb=" CG  MET A 595 "
        pdb=" SD  MET A 595 "
      ideal   model   delta    sigma   weight residual
     112.70  121.39   -8.69 3.00e+00 1.11e-01 8.38e+00
  angle pdb=" CA  MET A 493 "
        pdb=" CB  MET A 493 "
        pdb=" CG  MET A 493 "
      ideal   model   delta    sigma   weight residual
     114.10  119.28   -5.18 2.00e+00 2.50e-01 6.70e+00
  angle pdb=" N   ASP D 318 "
        pdb=" CA  ASP D 318 "
        pdb=" C   ASP D 318 "
      ideal   model   delta    sigma   weight residual
     113.72  110.18    3.54 1.52e+00 4.33e-01 5.42e+00
  ... (remaining 15899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.69: 6801
       35.69 -    71.39: 280
       71.39 -   107.08: 27
      107.08 -   142.78: 3
      142.78 -   178.47: 3
  Dihedral angle restraints: 7114
    sinusoidal: 2978
      harmonic: 4136
  Sorted by residual:
  dihedral pdb=" C2  TTP A 803 "
           pdb=" C1' TTP A 803 "
           pdb=" N1  TTP A 803 "
           pdb=" O4' TTP A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.32  120.15 -178.47     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" C2  TTP B 801 "
           pdb=" C1' TTP B 801 "
           pdb=" N1  TTP B 801 "
           pdb=" O4' TTP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  151.02  150.66     1      2.00e+01 2.50e-03 4.49e+01
  dihedral pdb=" C5' TTP A 803 "
           pdb=" O5' TTP A 803 "
           pdb=" PA  TTP A 803 "
           pdb=" O3A TTP A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.97   31.03  148.94     1      2.00e+01 2.50e-03 4.46e+01
  ... (remaining 7111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1004
       0.028 -    0.055: 440
       0.055 -    0.083: 152
       0.083 -    0.110: 74
       0.110 -    0.138: 20
  Chirality restraints: 1690
  Sorted by residual:
  chirality pdb=" CA  ILE A 652 "
            pdb=" N   ILE A 652 "
            pdb=" C   ILE A 652 "
            pdb=" CB  ILE A 652 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ILE B 652 "
            pdb=" N   ILE B 652 "
            pdb=" C   ILE B 652 "
            pdb=" CB  ILE B 652 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ASP A 398 "
            pdb=" N   ASP A 398 "
            pdb=" C   ASP A 398 "
            pdb=" CB  ASP A 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 1687 not shown)

  Planarity restraints: 2018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  35 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   SER B  35 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   SER B  35 "    0.009 2.00e-02 2.50e+03
        pdb=" N   TYR B  36 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 100 "   -0.011 2.00e-02 2.50e+03   8.51e-03 1.27e+00
        pdb=" CG  PHE B 100 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 100 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 100 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 579 "    0.018 5.00e-02 4.00e+02   2.73e-02 1.20e+00
        pdb=" N   PRO A 580 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 580 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 580 "    0.015 5.00e-02 4.00e+02
  ... (remaining 2015 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 168
        2.62 -     3.19: 10149
        3.19 -     3.76: 20484
        3.76 -     4.33: 29686
        4.33 -     4.90: 46484
  Nonbonded interactions: 106971
  Sorted by model distance:
  nonbonded pdb=" O2A TTP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" O2A TTP A 803 "
            pdb="MG    MG A 804 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" O   PRO A 616 "
            pdb=" OH  TYR A 626 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" O   PRO B 616 "
            pdb=" OH  TYR B 626 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O3G TTP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.175 2.170
  ... (remaining 106966 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: 0.05
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 6 through 688)
  selection = (chain 'B' and resid 6 through 688)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.160
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.050
  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:16.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
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      :  0.002   0.034  11776  Z= 0.111
  Angle     :  0.497   9.616  15904  Z= 0.260
  Chirality :  0.039   0.138   1690
  Planarity :  0.003   0.027   2018
  Dihedral  : 18.813 178.470   4454
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 19.53 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.89 (0.22), residues: 1386
  helix:  1.01 (0.20), residues: 678
  sheet:  0.40 (0.41), residues: 124
  loop :  0.32 (0.24), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B   9 
 HIS   0.002   0.000   HIS B 255 
 PHE   0.019   0.001   PHE B 100 
 TYR   0.017   0.001   TYR A 612 
 ARG   0.002   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13019 (  513)
  hydrogen bonds       : angle       6.54373 ( 1509)
  covalent geometry    : bond        0.00242 (11776)
  covalent geometry    : angle       0.49658 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7267 (tm-30)
REVERT: C  321 TYR cc_start: 0.8864 (m-80) cc_final: 0.8567 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 177
  average time/residue: 1.6716
  time to fit residues: 318.7758
Evaluate side-chains
  170 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  232 ASN
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 41 optimal weight:    0.1980
   chunk 65 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    1.4388

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 GLN
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.111734 restraints weight = 10657.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.42
r_work: 0.3065 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11776  Z= 0.200
  Angle     :  0.560   7.230  15904  Z= 0.296
  Chirality :  0.043   0.147   1690
  Planarity :  0.003   0.032   2018
  Dihedral  : 13.362 174.237   1665
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.53 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.96 (0.22), residues: 1386
  helix:  1.12 (0.20), residues: 668
  sheet: -0.03 (0.42), residues: 126
  loop :  0.40 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A   9 
 HIS   0.005   0.001   HIS A 438 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.016   0.002   TYR A 612 
 ARG   0.003   0.000   ARG B 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04326 (  513)
  hydrogen bonds       : angle       5.34327 ( 1509)
  covalent geometry    : bond        0.00457 (11776)
  covalent geometry    : angle       0.56005 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 166
  time to evaluate  : 1.602 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7354 (p)
REVERT: A  384 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8467 (pp20)
REVERT: A  402 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: A  518 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7610 (mp0)
REVERT: B   19 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8349 (mt0)
REVERT: B  214 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6947 (mtmm)
REVERT: B  665 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7623 (tmt170)
REVERT: C  321 TYR cc_start: 0.8332 (m-80) cc_final: 0.8094 (m-80)
  outliers start: 39
  outliers final: 14
  residues processed: 190
  average time/residue: 1.7379
  time to fit residues: 358.5254
Evaluate side-chains
  181 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  286 ASP
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  634 MET
Chi-restraints excluded: chain B residue  665 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 124 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.113331 restraints weight = 10886.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.44
r_work: 0.3093 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11776  Z= 0.157
  Angle     :  0.520   6.355  15904  Z= 0.274
  Chirality :  0.042   0.142   1690
  Planarity :  0.003   0.028   2018
  Dihedral  : 12.952 175.224   1654
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.59 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.90 (0.22), residues: 1386
  helix:  1.19 (0.20), residues: 668
  sheet: -0.47 (0.47), residues: 98
  loop :  0.27 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A   9 
 HIS   0.005   0.001   HIS A 438 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.014   0.001   TYR A 612 
 ARG   0.003   0.000   ARG A 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03859 (  513)
  hydrogen bonds       : angle       5.12278 ( 1509)
  covalent geometry    : bond        0.00356 (11776)
  covalent geometry    : angle       0.51973 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 2.028 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7387 (p)
REVERT: A   42 ASN cc_start: 0.8663 (m-40) cc_final: 0.8460 (m-40)
REVERT: A  110 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6295 (p0)
REVERT: A  384 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8457 (pp20)
REVERT: A  402 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6988 (tm-30)
REVERT: A  423 LYS cc_start: 0.8456 (mttm) cc_final: 0.8213 (mtpt)
REVERT: A  518 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7597 (mp0)
REVERT: B   19 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8325 (mt0)
REVERT: B  240 MET cc_start: 0.5165 (mpt) cc_final: 0.4936 (mpt)
REVERT: C  321 TYR cc_start: 0.8327 (m-80) cc_final: 0.8073 (m-80)
  outliers start: 34
  outliers final: 17
  residues processed: 186
  average time/residue: 1.4777
  time to fit residues: 296.2556
Evaluate side-chains
  183 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  634 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B 329 ASN
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.139607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.109284 restraints weight = 10776.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.42
r_work: 0.3033 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  11776  Z= 0.265
  Angle     :  0.605   7.325  15904  Z= 0.320
  Chirality :  0.046   0.181   1690
  Planarity :  0.004   0.033   2018
  Dihedral  : 13.225 171.188   1654
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.83 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.66 (0.21), residues: 1386
  helix:  0.90 (0.20), residues: 668
  sheet: -0.32 (0.42), residues: 126
  loop :  0.26 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 
 PHE   0.024   0.002   PHE B 100 
 TYR   0.017   0.002   TYR B 498 
 ARG   0.008   0.001   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04510 (  513)
  hydrogen bonds       : angle       5.35720 ( 1509)
  covalent geometry    : bond        0.00611 (11776)
  covalent geometry    : angle       0.60510 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 1.373 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7521 (p)
REVERT: A  384 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8527 (pp20)
REVERT: A  423 LYS cc_start: 0.8523 (mttm) cc_final: 0.8239 (mtpt)
REVERT: A  518 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7677 (mp0)
REVERT: B   19 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8404 (mt0)
REVERT: B   43 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7004 (mp10)
REVERT: B  239 GLN cc_start: 0.5013 (OUTLIER) cc_final: 0.4754 (mm110)
REVERT: B  384 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8339 (pm20)
REVERT: C  316 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6790 (mtpt)
  outliers start: 40
  outliers final: 20
  residues processed: 183
  average time/residue: 1.4380
  time to fit residues: 283.9355
Evaluate side-chains
  180 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 2.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  102 ASN
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  286 ASP
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.113313 restraints weight = 10871.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.44
r_work: 0.3092 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11776  Z= 0.144
  Angle     :  0.516   7.521  15904  Z= 0.272
  Chirality :  0.041   0.146   1690
  Planarity :  0.003   0.032   2018
  Dihedral  : 12.795 174.964   1654
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.12 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.81 (0.22), residues: 1386
  helix:  1.12 (0.20), residues: 670
  sheet: -0.58 (0.48), residues: 98
  loop :  0.24 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B   9 
 HIS   0.004   0.001   HIS B 438 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.015   0.001   TYR A 612 
 ARG   0.008   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  513)
  hydrogen bonds       : angle       5.07082 ( 1509)
  covalent geometry    : bond        0.00323 (11776)
  covalent geometry    : angle       0.51621 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 1.409 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7473 (p)
REVERT: A   42 ASN cc_start: 0.8666 (m-40) cc_final: 0.8445 (m-40)
REVERT: A  110 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6312 (p0)
REVERT: A  362 ASP cc_start: 0.8641 (m-30) cc_final: 0.8441 (m-30)
REVERT: A  384 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8469 (pp20)
REVERT: A  423 LYS cc_start: 0.8488 (mttm) cc_final: 0.8221 (mtpt)
REVERT: A  518 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7596 (mp0)
REVERT: B   15 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7468 (mt-10)
REVERT: B   25 GLN cc_start: 0.8464 (mt0) cc_final: 0.8218 (mt0)
REVERT: B   43 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7110 (mp10)
REVERT: B  240 MET cc_start: 0.5205 (mpt) cc_final: 0.4999 (mpt)
REVERT: B  384 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8250 (pp20)
REVERT: B  658 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8022 (mt)
REVERT: C  321 TYR cc_start: 0.8294 (m-80) cc_final: 0.8036 (m-80)
  outliers start: 35
  outliers final: 16
  residues processed: 189
  average time/residue: 1.3843
  time to fit residues: 282.4716
Evaluate side-chains
  187 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  311 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 124 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 126 optimal weight:    0.4980
   chunk 99 optimal weight:    5.9990
   chunk 123 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.142546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.112354 restraints weight = 10930.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.44
r_work: 0.3079 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11776  Z= 0.166
  Angle     :  0.536   7.365  15904  Z= 0.282
  Chirality :  0.042   0.143   1690
  Planarity :  0.003   0.037   2018
  Dihedral  : 12.746 174.789   1654
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.45 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.85 (0.22), residues: 1386
  helix:  1.12 (0.20), residues: 668
  sheet: -0.28 (0.43), residues: 126
  loop :  0.28 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.016   0.001   TYR A 612 
 ARG   0.008   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  513)
  hydrogen bonds       : angle       5.08733 ( 1509)
  covalent geometry    : bond        0.00379 (11776)
  covalent geometry    : angle       0.53583 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 1.253 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7469 (p)
REVERT: A   42 ASN cc_start: 0.8650 (m-40) cc_final: 0.8418 (m-40)
REVERT: A  362 ASP cc_start: 0.8664 (m-30) cc_final: 0.8459 (m-30)
REVERT: A  384 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8487 (pp20)
REVERT: A  402 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6988 (tm-30)
REVERT: A  423 LYS cc_start: 0.8532 (mttm) cc_final: 0.8267 (mtpt)
REVERT: A  518 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7595 (mp0)
REVERT: A  662 MET cc_start: 0.8454 (ptp) cc_final: 0.8147 (ptm)
REVERT: B   15 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7491 (mt-10)
REVERT: B   19 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8398 (mt0)
REVERT: B   43 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7113 (mp10)
REVERT: B  274 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6921 (ttm-80)
REVERT: B  384 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8282 (pp20)
REVERT: B  658 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8012 (mt)
REVERT: C  321 TYR cc_start: 0.8289 (m-80) cc_final: 0.8066 (m-80)
  outliers start: 32
  outliers final: 18
  residues processed: 188
  average time/residue: 1.3173
  time to fit residues: 266.8999
Evaluate side-chains
  187 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 161
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  311 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 109 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.111625 restraints weight = 10942.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 1.44
r_work: 0.3070 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11776  Z= 0.187
  Angle     :  0.553   8.556  15904  Z= 0.290
  Chirality :  0.043   0.145   1690
  Planarity :  0.003   0.040   2018
  Dihedral  : 12.772 173.856   1654
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.69 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.79 (0.22), residues: 1386
  helix:  1.05 (0.20), residues: 670
  sheet: -0.26 (0.42), residues: 126
  loop :  0.27 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.022   0.002   PHE B 100 
 TYR   0.018   0.002   TYR A 612 
 ARG   0.008   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03954 (  513)
  hydrogen bonds       : angle       5.13749 ( 1509)
  covalent geometry    : bond        0.00427 (11776)
  covalent geometry    : angle       0.55261 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 165
  time to evaluate  : 1.381 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7431 (p)
REVERT: A  362 ASP cc_start: 0.8692 (m-30) cc_final: 0.8477 (m-30)
REVERT: A  384 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8473 (pp20)
REVERT: A  402 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6961 (tm-30)
REVERT: A  423 LYS cc_start: 0.8506 (mttm) cc_final: 0.8230 (mtpt)
REVERT: A  518 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7642 (mp0)
REVERT: A  662 MET cc_start: 0.8456 (ptp) cc_final: 0.8214 (ptm)
REVERT: B   15 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7566 (mt-10)
REVERT: B   19 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8381 (mt0)
REVERT: B   43 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7102 (mp10)
REVERT: B  274 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6933 (ttm-80)
REVERT: B  384 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8497 (pm20)
REVERT: B  658 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8011 (mt)
REVERT: C  316 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6970 (mtpt)
  outliers start: 31
  outliers final: 18
  residues processed: 186
  average time/residue: 1.3641
  time to fit residues: 273.8115
Evaluate side-chains
  190 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 118 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.141739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.111605 restraints weight = 10920.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.43
r_work: 0.3073 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11776  Z= 0.181
  Angle     :  0.549   8.917  15904  Z= 0.288
  Chirality :  0.043   0.146   1690
  Planarity :  0.003   0.042   2018
  Dihedral  : 12.692 173.971   1654
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.77 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 (0.22), residues: 1386
  helix:  1.06 (0.20), residues: 670
  sheet: -0.28 (0.43), residues: 126
  loop :  0.28 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.022   0.002   PHE B 100 
 TYR   0.023   0.002   TYR A 612 
 ARG   0.009   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  513)
  hydrogen bonds       : angle       5.12102 ( 1509)
  covalent geometry    : bond        0.00413 (11776)
  covalent geometry    : angle       0.54902 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 1.490 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7468 (p)
REVERT: A  235 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7637 (mtt180)
REVERT: A  362 ASP cc_start: 0.8692 (m-30) cc_final: 0.8491 (m-30)
REVERT: A  384 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8483 (pp20)
REVERT: A  402 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6963 (tm-30)
REVERT: A  423 LYS cc_start: 0.8499 (mttm) cc_final: 0.8222 (mtpt)
REVERT: A  518 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7636 (mp0)
REVERT: A  662 MET cc_start: 0.8462 (ptp) cc_final: 0.8219 (ptm)
REVERT: B   15 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7512 (mt-10)
REVERT: B   19 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8402 (mt0)
REVERT: B   43 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7096 (mp10)
REVERT: B  274 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6934 (ttm-80)
REVERT: B  384 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8324 (pm20)
REVERT: B  658 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8007 (mt)
REVERT: C  321 TYR cc_start: 0.8224 (m-80) cc_final: 0.7905 (m-80)
  outliers start: 33
  outliers final: 20
  residues processed: 193
  average time/residue: 1.4090
  time to fit residues: 292.8763
Evaluate side-chains
  193 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  102 ASN
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  311 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0870
   chunk 91 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 134 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.113235 restraints weight = 10939.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.44
r_work: 0.3091 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11776  Z= 0.156
  Angle     :  0.537   9.549  15904  Z= 0.281
  Chirality :  0.042   0.141   1690
  Planarity :  0.003   0.040   2018
  Dihedral  : 12.528 175.431   1654
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.34 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.81 (0.22), residues: 1386
  helix:  1.14 (0.20), residues: 666
  sheet: -0.60 (0.48), residues: 102
  loop :  0.23 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.022   0.001   TYR A 612 
 ARG   0.009   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  513)
  hydrogen bonds       : angle       5.05428 ( 1509)
  covalent geometry    : bond        0.00356 (11776)
  covalent geometry    : angle       0.53671 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 1.277 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7453 (p)
REVERT: A   42 ASN cc_start: 0.8651 (m-40) cc_final: 0.8426 (m-40)
REVERT: A  362 ASP cc_start: 0.8690 (m-30) cc_final: 0.8454 (m-30)
REVERT: A  384 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8459 (pp20)
REVERT: A  402 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6996 (tm-30)
REVERT: A  423 LYS cc_start: 0.8437 (mttm) cc_final: 0.8173 (mtpt)
REVERT: A  518 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7614 (mp0)
REVERT: A  662 MET cc_start: 0.8456 (ptp) cc_final: 0.8216 (ptm)
REVERT: B   15 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7508 (mt-10)
REVERT: B   19 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8344 (mt0)
REVERT: B   43 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7107 (mp10)
REVERT: B  274 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6996 (ttm-80)
REVERT: B  384 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8301 (pm20)
REVERT: C  321 TYR cc_start: 0.8223 (m-80) cc_final: 0.7965 (m-80)
  outliers start: 29
  outliers final: 19
  residues processed: 190
  average time/residue: 1.3342
  time to fit residues: 273.4679
Evaluate side-chains
  194 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  102 ASN
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  277 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  311 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 111 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.142241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.111944 restraints weight = 10847.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.43
r_work: 0.3074 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11776  Z= 0.188
  Angle     :  0.565  10.417  15904  Z= 0.296
  Chirality :  0.043   0.145   1690
  Planarity :  0.003   0.042   2018
  Dihedral  : 12.527 174.017   1652
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.58 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.71 (0.22), residues: 1386
  helix:  1.05 (0.20), residues: 666
  sheet: -0.68 (0.47), residues: 102
  loop :  0.20 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.022   0.002   PHE B 100 
 TYR   0.026   0.002   TYR A 612 
 ARG   0.009   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  513)
  hydrogen bonds       : angle       5.13520 ( 1509)
  covalent geometry    : bond        0.00431 (11776)
  covalent geometry    : angle       0.56471 (15904)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 1.241 
Fit side-chains
REVERT: A   33 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7473 (p)
REVERT: A  235 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7635 (mtt180)
REVERT: A  362 ASP cc_start: 0.8689 (m-30) cc_final: 0.8472 (m-30)
REVERT: A  384 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8493 (pp20)
REVERT: A  402 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7002 (tm-30)
REVERT: A  423 LYS cc_start: 0.8509 (mttm) cc_final: 0.8233 (mtpt)
REVERT: A  518 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7643 (mp0)
REVERT: A  662 MET cc_start: 0.8466 (ptp) cc_final: 0.8221 (ptm)
REVERT: B   15 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7521 (mt-10)
REVERT: B   19 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8398 (mt0)
REVERT: B   43 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7097 (mp10)
REVERT: B  384 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8328 (pm20)
REVERT: C  316 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6932 (mtpt)
REVERT: C  321 TYR cc_start: 0.8208 (m-80) cc_final: 0.7976 (m-80)
  outliers start: 27
  outliers final: 18
  residues processed: 184
  average time/residue: 1.3809
  time to fit residues: 273.5474
Evaluate side-chains
  190 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  102 ASN
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  620 SER
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 137 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 132 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.144347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.114333 restraints weight = 10868.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.44
r_work: 0.3108 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11776  Z= 0.142
  Angle     :  0.530  10.315  15904  Z= 0.277
  Chirality :  0.041   0.139   1690
  Planarity :  0.003   0.039   2018
  Dihedral  : 12.296 176.645   1652
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.83 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.84 (0.22), residues: 1386
  helix:  1.18 (0.20), residues: 666
  sheet: -0.67 (0.47), residues: 102
  loop :  0.23 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B   9 
 HIS   0.004   0.001   HIS B 438 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.023   0.001   TYR A 612 
 ARG   0.009   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  513)
  hydrogen bonds       : angle       5.01388 ( 1509)
  covalent geometry    : bond        0.00324 (11776)
  covalent geometry    : angle       0.53036 (15904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9197.87 seconds
wall clock time: 162 minutes 27.65 seconds (9747.65 seconds total)