Starting phenix.real_space_refine
on Fri Jun  6 21:19:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1n_41818/06_2025/8u1n_41818.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1n_41818/06_2025/8u1n_41818.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1n_41818/06_2025/8u1n_41818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1n_41818/06_2025/8u1n_41818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1n_41818/06_2025/8u1n_41818.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1n_41818/06_2025/8u1n_41818.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.015
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       6      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    5158      2.51       5
     N    1366      2.21       5
     O    1604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8164
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4050
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 11, 'TRANS': 485}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4050
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 11, 'TRANS': 485}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.67
  Number of scatterers: 8164
  At special positions: 0
  Unit cell: (115.83, 120.978, 103.818, 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      28     16.00
     P       6     15.00
     Mg      2     11.99
     O    1604      8.00
     N    1366      7.00
     C    5158      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: 2.06
  Conformation dependent library (CDL) restraints added in 895.1 milliseconds
  

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      37.5% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 32
      removed outlier: 4.051A  pdb=" N   PHE A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 61
      removed outlier: 3.624A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 68
      removed outlier: 3.647A  pdb=" N   LEU A  65 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ASP A  66 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   SER A  67 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.654A  pdb=" N   ALA A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 138
    Processing helix  chain 'A' and resid 187 through 193
      removed outlier: 4.031A  pdb=" N   ALA A 190 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   GLU A 191 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 296 through 308
    Processing helix  chain 'A' and resid 370 through 374
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 3.681A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 416 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ASP A 421 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 443
      removed outlier: 6.972A  pdb=" N   LYS A 434 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   ASN A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LEU A 436 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS A 437 " --> pdb=" O   SER A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 452
      removed outlier: 3.834A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 473 through 475
      No H-bonds generated for 'chain 'A' and resid 473 through 475'
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.696A  pdb=" N   ALA A 494 " --> pdb=" O   ASP A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 505
      removed outlier: 3.591A  pdb=" N   LYS A 504 " --> pdb=" O   ARG A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 524
    Processing helix  chain 'B' and resid 20 through 32
      removed outlier: 3.699A  pdb=" N   LEU B  24 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   MET B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   SER B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE B  32 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 61
      removed outlier: 3.819A  pdb=" N   THR B  60 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASP B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 101
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 3.763A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 138
      removed outlier: 3.829A  pdb=" N   SER B 135 " --> pdb=" O   GLY B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 193
    Processing helix  chain 'B' and resid 194 through 206
    Processing helix  chain 'B' and resid 296 through 309
      removed outlier: 4.240A  pdb=" N   TYR B 300 " --> pdb=" O   THR B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 374
    Processing helix  chain 'B' and resid 396 through 418
    Processing helix  chain 'B' and resid 421 through 443
      removed outlier: 6.937A  pdb=" N   LYS B 434 " --> pdb=" O   GLU B 430 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ASN B 435 " --> pdb=" O   GLN B 431 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   LEU B 436 " --> pdb=" O   PHE B 432 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 454
    Processing helix  chain 'B' and resid 468 through 474
      removed outlier: 3.615A  pdb=" N   VAL B 472 " --> pdb=" O   LEU B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 495
      removed outlier: 3.725A  pdb=" N   VAL B 493 " --> pdb=" O   ASN B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 504
      removed outlier: 3.952A  pdb=" N   ARG B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   VAL B 502 " --> pdb=" O   PHE B 498 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS B 504 " --> pdb=" O   GLU B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 521
      removed outlier: 3.588A  pdb=" N   VAL B 521 " --> pdb=" O   ASP B 517 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 3.592A  pdb=" N   PHE A  15 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE B 165 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG B 168 " --> pdb=" O   MET B 156 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   SER B 159 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL B 143 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ARG B 142 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19
      removed outlier: 7.040A  pdb=" N   GLN A  18 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215
      removed outlier: 7.233A  pdb=" N   ILE A  73 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASP A  88 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 178 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ARG A 142 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG A 168 " --> pdb=" O   MET A 156 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322
      removed outlier: 6.641A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   VAL A 317 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A 332 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   HIS A 319 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   ALA A 330 " --> pdb=" O   HIS A 319 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   SER A 321 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   PHE A 328 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 456
    Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485
      removed outlier: 7.439A  pdb=" N   TYR A 483 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 322
      removed outlier: 3.575A  pdb=" N   LEU B 332 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE B 320 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   MET B 362 " --> pdb=" O   LEU B 354 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   VAL B 356 " --> pdb=" O   PHE B 360 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   PHE B 360 " --> pdb=" O   VAL B 356 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 456
    Processing sheet with id=AB1, first strand: chain 'B' and resid 482 through 483
      removed outlier: 6.015A  pdb=" N   ILE B 482 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)

    293 hydrogen bonds defined for protein.
    798 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: 2.39

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2661
        1.34 -     1.46: 1767
        1.46 -     1.58: 3826
        1.58 -     1.70: 4
        1.70 -     1.82: 48
  Bond restraints: 8306
  Sorted by residual:
  bond pdb=" C5' ATP B 801 "
       pdb=" O5' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.443  1.221  0.222 1.00e-02 1.00e+04 4.93e+02
  bond pdb=" C5' ATP A 801 "
       pdb=" O5' ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.443  1.222  0.221 1.00e-02 1.00e+04 4.90e+02
  bond pdb=" C1' ATP B 801 "
       pdb=" O4' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.416  1.359  0.057 1.30e-02 5.92e+03 1.94e+01
  bond pdb=" C4' ATP B 801 "
       pdb=" O4' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.444  1.397  0.047 1.10e-02 8.26e+03 1.86e+01
  bond pdb=" C3' ATP B 801 "
       pdb=" O3' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.423  1.377  0.046 1.10e-02 8.26e+03 1.73e+01
  ... (remaining 8301 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.88: 11152
        6.88 -    13.76: 18
       13.76 -    20.64: 4
       20.64 -    27.53: 1
       27.53 -    34.41: 7
  Bond angle restraints: 11182
  Sorted by residual:
  angle pdb=" C5' ATP A 801 "
        pdb=" O5' ATP A 801 "
        pdb=" PA  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     121.27  155.68  -34.41 1.00e+00 1.00e+00 1.18e+03
  angle pdb=" C5' ATP B 801 "
        pdb=" O5' ATP B 801 "
        pdb=" PA  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     121.27  154.53  -33.26 1.00e+00 1.00e+00 1.11e+03
  angle pdb=" C3' ATP A 801 "
        pdb=" C4' ATP A 801 "
        pdb=" C5' ATP A 801 "
      ideal   model   delta    sigma   weight residual
     115.19   82.86   32.33 1.76e+00 3.23e-01 3.37e+02
  angle pdb=" C3' ATP B 801 "
        pdb=" C4' ATP B 801 "
        pdb=" C5' ATP B 801 "
      ideal   model   delta    sigma   weight residual
     115.19   84.99   30.20 1.76e+00 3.23e-01 2.95e+02
  angle pdb=" C4' ATP A 801 "
        pdb=" C5' ATP A 801 "
        pdb=" O5' ATP A 801 "
      ideal   model   delta    sigma   weight residual
     108.83  138.61  -29.78 2.33e+00 1.85e-01 1.64e+02
  ... (remaining 11177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4300
       17.84 -    35.67: 613
       35.67 -    53.51: 153
       53.51 -    71.34: 34
       71.34 -    89.18: 16
  Dihedral angle restraints: 5116
    sinusoidal: 2194
      harmonic: 2922
  Sorted by residual:
  dihedral pdb=" CA  TYR B 511 "
           pdb=" C   TYR B 511 "
           pdb=" N   MET B 512 "
           pdb=" CA  MET B 512 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.33  -22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  TYR A 507 "
           pdb=" C   TYR A 507 "
           pdb=" N   GLU A 508 "
           pdb=" CA  GLU A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.28  -21.72     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  GLU B 514 "
           pdb=" C   GLU B 514 "
           pdb=" N   PRO B 515 "
           pdb=" CA  PRO B 515 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.58  -20.42     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1161
       0.096 -    0.192: 55
       0.192 -    0.288: 4
       0.288 -    0.384: 0
       0.384 -    0.480: 2
  Chirality restraints: 1222
  Sorted by residual:
  chirality pdb=" C4' ATP B 801 "
            pdb=" C3' ATP B 801 "
            pdb=" C5' ATP B 801 "
            pdb=" O4' ATP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.97    0.48 2.00e-01 2.50e+01 5.75e+00
  chirality pdb=" C4' ATP A 801 "
            pdb=" C3' ATP A 801 "
            pdb=" C5' ATP A 801 "
            pdb=" O4' ATP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.95    0.46 2.00e-01 2.50e+01 5.26e+00
  chirality pdb=" C3' ATP A 801 "
            pdb=" C2' ATP A 801 "
            pdb=" C4' ATP A 801 "
            pdb=" O3' ATP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 1219 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 514 "   -0.058 5.00e-02 4.00e+02   8.71e-02 1.21e+01
        pdb=" N   PRO B 515 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO B 515 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 515 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 285 "   -0.036 5.00e-02 4.00e+02   5.54e-02 4.92e+00
        pdb=" N   PRO B 286 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 286 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 286 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  76 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO B  77 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B  77 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  77 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 86
        2.49 -     3.09: 5771
        3.09 -     3.69: 12970
        3.69 -     4.30: 17680
        4.30 -     4.90: 27978
  Nonbonded interactions: 64485
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.883 2.170
  nonbonded pdb=" O5' ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.893 2.170
  nonbonded pdb=" O2A ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.914 2.170
  nonbonded pdb=" O2B ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.915 2.170
  nonbonded pdb=" O2G ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.962 2.170
  ... (remaining 64480 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.110
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
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      :  0.005   0.222   8306  Z= 0.417
  Angle     :  1.169  34.407  11182  Z= 0.710
  Chirality :  0.048   0.480   1222
  Planarity :  0.004   0.087   1426
  Dihedral  : 17.981  89.180   3232
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.00 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.26), residues: 986
  helix: -0.15 (0.29), residues: 317
  sheet:  0.20 (0.44), residues: 158
  loop : -1.53 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 481 
 PHE   0.010   0.001   PHE B 165 
 TYR   0.023   0.001   TYR B 519 
 ARG   0.004   0.000   ARG B 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21833 (  293)
  hydrogen bonds       : angle       8.04466 (  798)
  covalent geometry    : bond        0.00525 ( 8306)
  covalent geometry    : angle       1.16929 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 LEU cc_start: 0.8395 (mt) cc_final: 0.8118 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1658
  time to fit residues: 14.0652
Evaluate side-chains
  45 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 41 optimal weight:   40.0000
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    0.3980
   chunk 39 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 ASN
A 479 GLN
A 492 GLN
B 149 HIS
** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.067005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.047284 restraints weight = 42755.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.049291 restraints weight = 23433.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.050565 restraints weight = 16261.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8306  Z= 0.175
  Angle     :  0.635   7.756  11182  Z= 0.333
  Chirality :  0.043   0.147   1222
  Planarity :  0.004   0.056   1426
  Dihedral  : 10.409  88.869   1150
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 22.99 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.27), residues: 986
  helix: -0.05 (0.28), residues: 318
  sheet:  0.07 (0.42), residues: 176
  loop : -1.58 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 311 
 HIS   0.006   0.001   HIS A 481 
 PHE   0.010   0.001   PHE B  84 
 TYR   0.019   0.002   TYR A 527 
 ARG   0.004   0.001   ARG B 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04880 (  293)
  hydrogen bonds       : angle       6.23088 (  798)
  covalent geometry    : bond        0.00391 ( 8306)
  covalent geometry    : angle       0.63468 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 48
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8244 (mp0)
REVERT: A  117 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8529 (mp)
REVERT: A  267 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.6994 (pptt)
REVERT: A  508 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5850 (mt-10)
REVERT: B   84 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6205 (t80)
REVERT: B  152 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8780 (t70)
REVERT: B  512 MET cc_start: 0.5639 (tmm) cc_final: 0.5130 (tmm)
  outliers start: 38
  outliers final: 15
  residues processed: 83
  average time/residue: 0.1586
  time to fit residues: 20.1365
Evaluate side-chains
  67 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  510 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.065397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.045720 restraints weight = 44012.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.047706 restraints weight = 24009.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.048992 restraints weight = 16654.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   8306  Z= 0.239
  Angle     :  0.685   8.096  11182  Z= 0.355
  Chirality :  0.044   0.143   1222
  Planarity :  0.005   0.050   1426
  Dihedral  :  9.896  84.223   1150
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 18.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 24.44 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.26), residues: 986
  helix: -0.28 (0.28), residues: 314
  sheet: -0.16 (0.43), residues: 174
  loop : -1.81 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 157 
 HIS   0.006   0.002   HIS A 481 
 PHE   0.012   0.002   PHE B 165 
 TYR   0.016   0.002   TYR A 428 
 ARG   0.004   0.001   ARG B 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04948 (  293)
  hydrogen bonds       : angle       6.13133 (  798)
  covalent geometry    : bond        0.00539 ( 8306)
  covalent geometry    : angle       0.68480 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 44
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (mp0)
REVERT: A   93 MET cc_start: 0.7207 (mmt) cc_final: 0.6549 (mmt)
REVERT: A  117 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8546 (mp)
REVERT: A  267 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.6890 (pptt)
REVERT: A  514 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5600 (pm20)
REVERT: A  527 TYR cc_start: 0.8144 (t80) cc_final: 0.7672 (t80)
REVERT: B   84 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6337 (t80)
REVERT: B  152 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8698 (t70)
REVERT: B  300 TYR cc_start: 0.5361 (OUTLIER) cc_final: 0.4895 (m-10)
REVERT: B  512 MET cc_start: 0.5797 (tmm) cc_final: 0.5572 (tmm)
  outliers start: 50
  outliers final: 29
  residues processed: 89
  average time/residue: 0.1579
  time to fit residues: 21.3269
Evaluate side-chains
  78 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 42
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  411 CYS
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  429 TYR
Chi-restraints excluded: chain B residue  510 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 92 optimal weight:    0.0970
   chunk 57 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.067446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.047902 restraints weight = 42819.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.049966 restraints weight = 23028.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.051274 restraints weight = 15826.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8306  Z= 0.117
  Angle     :  0.575   7.344  11182  Z= 0.301
  Chirality :  0.042   0.151   1222
  Planarity :  0.004   0.048   1426
  Dihedral  :  9.448  88.255   1150
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.78 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.26), residues: 986
  helix:  0.16 (0.29), residues: 309
  sheet:  0.06 (0.44), residues: 174
  loop : -1.80 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 157 
 HIS   0.005   0.001   HIS A 441 
 PHE   0.009   0.001   PHE A 432 
 TYR   0.012   0.001   TYR A 428 
 ARG   0.003   0.000   ARG B 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  293)
  hydrogen bonds       : angle       5.66039 (  798)
  covalent geometry    : bond        0.00258 ( 8306)
  covalent geometry    : angle       0.57490 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 47
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.6520 (mmt) cc_final: 0.5809 (mmt)
REVERT: A  117 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8484 (mp)
REVERT: A  267 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6766 (pptt)
REVERT: A  508 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.6076 (mt-10)
REVERT: A  514 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5487 (pm20)
REVERT: A  527 TYR cc_start: 0.8008 (t80) cc_final: 0.7631 (t80)
REVERT: B   93 MET cc_start: 0.7833 (mmt) cc_final: 0.7001 (mmt)
REVERT: B  300 TYR cc_start: 0.5068 (OUTLIER) cc_final: 0.4586 (m-10)
REVERT: B  342 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5299 (tp)
  outliers start: 33
  outliers final: 16
  residues processed: 75
  average time/residue: 0.1647
  time to fit residues: 18.7207
Evaluate side-chains
  66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  519 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   chunk 31 optimal weight:    0.4980
   chunk 93 optimal weight:   30.0000
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.067381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.047900 restraints weight = 42847.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.049948 restraints weight = 23245.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.051260 restraints weight = 16008.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8306  Z= 0.122
  Angle     :  0.573   8.880  11182  Z= 0.297
  Chirality :  0.041   0.145   1222
  Planarity :  0.003   0.047   1426
  Dihedral  :  9.342  86.353   1150
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 26.12 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 986
  helix:  0.25 (0.29), residues: 310
  sheet:  0.09 (0.44), residues: 174
  loop : -1.76 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 157 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.009   0.001   PHE B 498 
 TYR   0.010   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  293)
  hydrogen bonds       : angle       5.49900 (  798)
  covalent geometry    : bond        0.00273 ( 8306)
  covalent geometry    : angle       0.57316 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 46
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.6467 (mmt) cc_final: 0.6125 (mmt)
REVERT: A  117 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8490 (mp)
REVERT: A  267 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6759 (pptt)
REVERT: A  508 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5787 (mt-10)
REVERT: A  514 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5460 (pm20)
REVERT: A  527 TYR cc_start: 0.8091 (t80) cc_final: 0.7715 (t80)
REVERT: B  152 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8829 (t70)
REVERT: B  300 TYR cc_start: 0.5068 (OUTLIER) cc_final: 0.4823 (m-10)
REVERT: B  342 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5320 (tp)
REVERT: B  512 MET cc_start: 0.5657 (tmm) cc_final: 0.5412 (tmm)
  outliers start: 35
  outliers final: 17
  residues processed: 77
  average time/residue: 0.1781
  time to fit residues: 21.6316
Evaluate side-chains
  67 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 43
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  376 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:   20.0000
   chunk 71 optimal weight:    0.0000
   chunk 76 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.065157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.045920 restraints weight = 44036.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.047842 restraints weight = 24399.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.049051 restraints weight = 17074.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8306  Z= 0.251
  Angle     :  0.701   9.289  11182  Z= 0.362
  Chirality :  0.044   0.142   1222
  Planarity :  0.004   0.048   1426
  Dihedral  :  9.767  79.118   1150
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 19.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.56 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.26), residues: 986
  helix: -0.11 (0.28), residues: 314
  sheet: -0.16 (0.43), residues: 174
  loop : -1.83 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 311 
 HIS   0.005   0.002   HIS A 441 
 PHE   0.015   0.002   PHE B 360 
 TYR   0.028   0.002   TYR A 428 
 ARG   0.004   0.001   ARG B 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04685 (  293)
  hydrogen bonds       : angle       5.93681 (  798)
  covalent geometry    : bond        0.00562 ( 8306)
  covalent geometry    : angle       0.70126 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 42
  time to evaluate  : 2.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.7309 (mmt) cc_final: 0.6110 (mmt)
REVERT: A  125 MET cc_start: 0.8632 (mmm) cc_final: 0.8206 (mmm)
REVERT: A  267 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.6841 (pptt)
REVERT: A  514 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5268 (mp0)
REVERT: A  527 TYR cc_start: 0.8189 (t80) cc_final: 0.7883 (t80)
REVERT: B   84 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6241 (t80)
REVERT: B   93 MET cc_start: 0.7876 (mmt) cc_final: 0.7270 (mmt)
REVERT: B  152 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8816 (t70)
REVERT: B  342 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.5425 (tp)
REVERT: B  456 TYR cc_start: 0.8685 (m-80) cc_final: 0.8140 (m-80)
REVERT: B  512 MET cc_start: 0.5870 (tmm) cc_final: 0.5581 (tmm)
  outliers start: 49
  outliers final: 29
  residues processed: 87
  average time/residue: 0.1900
  time to fit residues: 26.2294
Evaluate side-chains
  75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 41
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  429 TYR
Chi-restraints excluded: chain B residue  532 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 91 optimal weight:   10.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.067731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.048077 restraints weight = 42892.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.050230 restraints weight = 22560.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.051580 restraints weight = 15298.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8306  Z= 0.109
  Angle     :  0.593   9.219  11182  Z= 0.307
  Chirality :  0.042   0.145   1222
  Planarity :  0.003   0.050   1426
  Dihedral  :  9.300  87.527   1150
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 28.24 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.27), residues: 986
  helix:  0.26 (0.29), residues: 316
  sheet:  0.12 (0.44), residues: 174
  loop : -1.80 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 157 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.008   0.001   PHE A 432 
 TYR   0.018   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  293)
  hydrogen bonds       : angle       5.46362 (  798)
  covalent geometry    : bond        0.00238 ( 8306)
  covalent geometry    : angle       0.59265 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 47
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.6206 (mmt) cc_final: 0.4969 (mmt)
REVERT: A  117 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8423 (mp)
REVERT: A  267 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6701 (pptt)
REVERT: A  514 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5731 (pm20)
REVERT: A  527 TYR cc_start: 0.8107 (t80) cc_final: 0.7790 (t80)
REVERT: B  152 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (t0)
REVERT: B  342 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5210 (tp)
  outliers start: 24
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1545
  time to fit residues: 17.0191
Evaluate side-chains
  65 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 55 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 94 optimal weight:    0.1980
   chunk 88 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    2.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 441 HIS
** B 492 GLN ** 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 = 0.3769 r_free = 0.3769 target = 0.066415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.046967 restraints weight = 43842.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.048961 restraints weight = 23569.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.050251 restraints weight = 16264.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8306  Z= 0.155
  Angle     :  0.606   9.886  11182  Z= 0.313
  Chirality :  0.042   0.139   1222
  Planarity :  0.004   0.049   1426
  Dihedral  :  9.425  84.323   1150
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.90 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.27), residues: 986
  helix:  0.31 (0.29), residues: 315
  sheet:  0.03 (0.44), residues: 171
  loop : -1.77 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 311 
 HIS   0.005   0.001   HIS A 441 
 PHE   0.016   0.001   PHE B 498 
 TYR   0.019   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03834 (  293)
  hydrogen bonds       : angle       5.50758 (  798)
  covalent geometry    : bond        0.00349 ( 8306)
  covalent geometry    : angle       0.60605 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 44
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8435 (mp)
REVERT: A  267 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6724 (pptt)
REVERT: A  514 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5879 (pm20)
REVERT: A  527 TYR cc_start: 0.8145 (t80) cc_final: 0.7811 (t80)
REVERT: B   84 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6206 (t80)
REVERT: B  152 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8754 (t70)
REVERT: B  342 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5197 (tp)
REVERT: B  512 MET cc_start: 0.5436 (tmm) cc_final: 0.5069 (tmm)
  outliers start: 26
  outliers final: 17
  residues processed: 68
  average time/residue: 0.1455
  time to fit residues: 15.7207
Evaluate side-chains
  67 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 44
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0470
   chunk 76 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.5484

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.067411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.047752 restraints weight = 44019.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.049916 restraints weight = 23168.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.051291 restraints weight = 15669.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8306  Z= 0.117
  Angle     :  0.586   9.733  11182  Z= 0.300
  Chirality :  0.041   0.141   1222
  Planarity :  0.003   0.050   1426
  Dihedral  :  9.310  86.878   1150
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.79 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.27), residues: 986
  helix:  0.40 (0.29), residues: 315
  sheet:  0.07 (0.44), residues: 172
  loop : -1.75 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.012   0.001   PHE B 498 
 TYR   0.016   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 501 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  293)
  hydrogen bonds       : angle       5.34960 (  798)
  covalent geometry    : bond        0.00263 ( 8306)
  covalent geometry    : angle       0.58592 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8423 (mp)
REVERT: A  267 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6597 (pptt)
REVERT: A  514 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5705 (pm20)
REVERT: A  527 TYR cc_start: 0.8066 (t80) cc_final: 0.7712 (t80)
REVERT: B   84 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6084 (t80)
REVERT: B  152 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8827 (t70)
REVERT: B  342 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5209 (tp)
REVERT: B  512 MET cc_start: 0.5304 (tmm) cc_final: 0.4937 (tmm)
  outliers start: 26
  outliers final: 17
  residues processed: 68
  average time/residue: 0.1480
  time to fit residues: 15.9065
Evaluate side-chains
  66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 43
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.067069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.046525 restraints weight = 41693.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.048748 restraints weight = 21549.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.050190 restraints weight = 14431.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8306  Z= 0.102
  Angle     :  0.571  10.227  11182  Z= 0.292
  Chirality :  0.041   0.143   1222
  Planarity :  0.003   0.049   1426
  Dihedral  :  9.303  85.762   1150
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 28.57 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.88 (0.27), residues: 986
  helix:  0.66 (0.30), residues: 308
  sheet:  0.16 (0.44), residues: 172
  loop : -1.70 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 157 
 HIS   0.004   0.001   HIS A 171 
 PHE   0.008   0.001   PHE B 498 
 TYR   0.012   0.001   TYR A 428 
 ARG   0.002   0.000   ARG B 501 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  293)
  hydrogen bonds       : angle       5.16532 (  798)
  covalent geometry    : bond        0.00230 ( 8306)
  covalent geometry    : angle       0.57103 (11182)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 46
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8444 (mp)
REVERT: A  267 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6581 (pptt)
REVERT: A  514 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5644 (mp0)
REVERT: A  527 TYR cc_start: 0.8321 (t80) cc_final: 0.7941 (t80)
REVERT: B   84 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6241 (t80)
REVERT: B   93 MET cc_start: 0.7063 (mmt) cc_final: 0.6822 (mmp)
REVERT: B  342 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5134 (tp)
REVERT: B  512 MET cc_start: 0.5387 (tmm) cc_final: 0.4996 (tmm)
  outliers start: 22
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1495
  time to fit residues: 15.8917
Evaluate side-chains
  64 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 83 optimal weight:    0.0870
   chunk 18 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.066092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.046655 restraints weight = 44369.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.048646 restraints weight = 23913.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.049924 restraints weight = 16388.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8306  Z= 0.182
  Angle     :  0.638  10.170  11182  Z= 0.325
  Chirality :  0.042   0.138   1222
  Planarity :  0.004   0.048   1426
  Dihedral  :  9.463  77.879   1150
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 28.01 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.27), residues: 986
  helix:  0.41 (0.29), residues: 315
  sheet:  0.07 (0.43), residues: 173
  loop : -1.74 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 311 
 HIS   0.005   0.001   HIS B 205 
 PHE   0.011   0.001   PHE B 360 
 TYR   0.027   0.001   TYR A 428 
 ARG   0.004   0.000   ARG B 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  293)
  hydrogen bonds       : angle       5.42896 (  798)
  covalent geometry    : bond        0.00408 ( 8306)
  covalent geometry    : angle       0.63798 (11182)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3446.49 seconds
wall clock time: 62 minutes 2.89 seconds (3722.89 seconds total)