Starting phenix.real_space_refine
on Wed Feb 12 17:54:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1n_41818/02_2025/8u1n_41818.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1n_41818/02_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_41818/02_2025/8u1n_41818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1n_41818/02_2025/8u1n_41818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1n_41818/02_2025/8u1n_41818.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1n_41818/02_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-5592/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: 4.96, per 1000 atoms: 0.61
  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.85
  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: 2.26

  Time building geometry restraints manager: 2.52 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:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     20.660
  Find NCS groups from input model:        0.290
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.280
-------------------------------------------------------------------------------
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= 0.330
  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 

*********************** 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  : 0.924 
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: 0.1733
  time to fit residues: 14.5139
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  : 0.908 
-------------------------------------------------------------------------------
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 = 50)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.047272 restraints weight = 42755.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.049270 restraints weight = 23480.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.050538 restraints weight = 16310.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
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= 0.255
  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 

*********************** 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  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8489 (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: 0.7929 (OUTLIER) cc_final: 0.6995 (pptt)
REVERT: A  508 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5851 (mt-10)
REVERT: B   84 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6204 (t80)
REVERT: B  152 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8781 (t70)
REVERT: B  512 MET cc_start: 0.5638 (tmm) cc_final: 0.5129 (tmm)
  outliers start: 38
  outliers final: 15
  residues processed: 83
  average time/residue: 0.1610
  time to fit residues: 20.2938
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  : 0.887 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 22 optimal weight:    7.9990
   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 = 0.3742 r_free = 0.3742 target = 0.065452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.045766 restraints weight = 44008.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.047758 restraints weight = 24054.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.048998 restraints weight = 16644.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   8306  Z= 0.348
  Angle     :  0.683   8.216  11182  Z= 0.355
  Chirality :  0.044   0.143   1222
  Planarity :  0.005   0.050   1426
  Dihedral  :  9.889  84.034   1150
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 24.55 %
    Favored  : 70.09 %
  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: -1.49 (0.26), residues: 986
  helix: -0.27 (0.28), residues: 314
  sheet: -0.14 (0.43), residues: 174
  loop : -1.79 (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   0.005   0.001   ARG B 329 

*********************** 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
  92 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 44
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8236 (mp0)
REVERT: A   93 MET cc_start: 0.7184 (mmt) cc_final: 0.6506 (mmt)
REVERT: A  117 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8546 (mp)
REVERT: A  156 MET cc_start: 0.7893 (pmm) cc_final: 0.7692 (mpp)
REVERT: A  267 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6879 (pptt)
REVERT: A  514 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5589 (pm20)
REVERT: A  527 TYR cc_start: 0.8137 (t80) cc_final: 0.7675 (t80)
REVERT: B   84 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6331 (t80)
REVERT: B  152 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8698 (t70)
REVERT: B  300 TYR cc_start: 0.5363 (OUTLIER) cc_final: 0.4897 (m-10)
REVERT: B  512 MET cc_start: 0.5794 (tmm) cc_final: 0.5570 (tmm)
  outliers start: 48
  outliers final: 29
  residues processed: 87
  average time/residue: 0.1529
  time to fit residues: 20.4721
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  : 0.919 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 92 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 42 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.067172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.047696 restraints weight = 42756.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.049749 restraints weight = 23082.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.051003 restraints weight = 15880.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1868

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= 0.179
  Angle     :  0.578   7.409  11182  Z= 0.303
  Chirality :  0.042   0.148   1222
  Planarity :  0.004   0.049   1426
  Dihedral  :  9.472  86.567   1150
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.56 %
    Favored  : 70.31 %
  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: -1.23 (0.26), residues: 986
  helix:  0.15 (0.29), residues: 309
  sheet:  0.03 (0.44), residues: 174
  loop : -1.79 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   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 

*********************** 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
  85 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 48
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.6632 (mmt) cc_final: 0.5880 (mmt)
REVERT: A  117 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8487 (mp)
REVERT: A  267 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6762 (pptt)
REVERT: A  508 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6096 (mt-10)
REVERT: A  514 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5493 (pm20)
REVERT: A  527 TYR cc_start: 0.7972 (t80) cc_final: 0.7634 (t80)
REVERT: B   93 MET cc_start: 0.7819 (mmt) cc_final: 0.7016 (mmt)
REVERT: B  152 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (t70)
REVERT: B  300 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.4580 (m-10)
REVERT: B  342 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5300 (tp)
  outliers start: 37
  outliers final: 18
  residues processed: 80
  average time/residue: 0.1781
  time to fit residues: 21.1410
Evaluate side-chains
  69 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 44
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  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  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  152 ASP
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  434 LYS
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:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 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 = 0.3750 r_free = 0.3750 target = 0.065666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.046103 restraints weight = 44006.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.048103 restraints weight = 23906.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.049372 restraints weight = 16563.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8306  Z= 0.295
  Angle     :  0.644   8.901  11182  Z= 0.334
  Chirality :  0.043   0.142   1222
  Planarity :  0.004   0.050   1426
  Dihedral  :  9.625  79.249   1150
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 26.00 %
    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: -1.40 (0.26), residues: 986
  helix: -0.04 (0.28), residues: 315
  sheet: -0.13 (0.43), residues: 175
  loop : -1.85 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 311 
 HIS   0.005   0.001   HIS A 441 
 PHE   0.012   0.002   PHE B 360 
 TYR   0.013   0.002   TYR A 428 
 ARG   0.003   0.000   ARG B 329 

*********************** 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
  90 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 43
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.7320 (mmt) cc_final: 0.6538 (mmt)
REVERT: A  117 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (mp)
REVERT: A  125 MET cc_start: 0.8684 (mmm) cc_final: 0.8187 (mmm)
REVERT: A  267 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.6857 (pptt)
REVERT: A  514 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5771 (pm20)
REVERT: A  527 TYR cc_start: 0.8145 (t80) cc_final: 0.7741 (t80)
REVERT: B   84 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6261 (t80)
REVERT: B  152 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8807 (t70)
REVERT: B  300 TYR cc_start: 0.5254 (OUTLIER) cc_final: 0.4911 (m-10)
REVERT: B  342 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5379 (tp)
REVERT: B  512 MET cc_start: 0.5910 (tmm) cc_final: 0.5637 (tmm)
  outliers start: 47
  outliers final: 28
  residues processed: 87
  average time/residue: 0.1640
  time to fit residues: 21.6996
Evaluate side-chains
  79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 44
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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  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  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   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  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  342 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  434 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
** 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 = 0.3696 r_free = 0.3696 target = 0.063782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.044405 restraints weight = 46046.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.046257 restraints weight = 25861.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.047412 restraints weight = 18254.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.092   8306  Z= 0.518
  Angle     :  0.838  12.189  11182  Z= 0.432
  Chirality :  0.047   0.149   1222
  Planarity :  0.005   0.058   1426
  Dihedral  : 10.191  73.615   1150
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 25.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 25.67 %
    Favored  : 67.08 %
  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: -1.98 (0.26), residues: 986
  helix: -0.65 (0.27), residues: 313
  sheet: -0.58 (0.43), residues: 174
  loop : -2.04 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP A 157 
 HIS   0.007   0.002   HIS A 146 
 PHE   0.020   0.002   PHE B 303 
 TYR   0.018   0.003   TYR A 428 
 ARG   0.006   0.001   ARG B 329 

*********************** 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
  103 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 38
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.8308 (mmt) cc_final: 0.8058 (mmt)
REVERT: A  117 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8542 (mp)
REVERT: A  267 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.6763 (pptt)
REVERT: A  514 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5398 (mp0)
REVERT: A  527 TYR cc_start: 0.8252 (t80) cc_final: 0.7983 (t80)
REVERT: B   84 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6345 (t80)
REVERT: B  152 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8614 (t70)
REVERT: B  177 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7434 (ttp80)
REVERT: B  300 TYR cc_start: 0.5451 (OUTLIER) cc_final: 0.4885 (m-10)
  outliers start: 65
  outliers final: 40
  residues processed: 98
  average time/residue: 0.1864
  time to fit residues: 26.9761
Evaluate side-chains
  82 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 35
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
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  198 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  352 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  434 LYS
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   40 LEU
Chi-restraints excluded: chain B residue   54 ILE
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  145 VAL
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  177 ARG
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  182 VAL
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  418 LEU
Chi-restraints excluded: chain B residue  429 TYR
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  523 GLN
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:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   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 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 = 0.3707 r_free = 0.3707 target = 0.065499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.044906 restraints weight = 42287.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.047094 restraints weight = 21692.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.048521 restraints weight = 14538.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8306  Z= 0.170
  Angle     :  0.641   9.842  11182  Z= 0.331
  Chirality :  0.043   0.149   1222
  Planarity :  0.004   0.053   1426
  Dihedral  :  9.492  88.495   1150
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 29.02 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.50 (0.26), residues: 986
  helix: -0.04 (0.29), residues: 317
  sheet: -0.21 (0.44), residues: 174
  loop : -1.97 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 157 
 HIS   0.005   0.001   HIS A 146 
 PHE   0.009   0.001   PHE A 432 
 TYR   0.012   0.001   TYR A 428 
 ARG   0.002   0.000   ARG A  55 

*********************** 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
  72 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 44
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7925 (m-80)
REVERT: A   93 MET cc_start: 0.7341 (mmt) cc_final: 0.7002 (mmp)
REVERT: A  117 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8475 (mp)
REVERT: A  267 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6762 (pptt)
REVERT: A  463 ASP cc_start: 0.9177 (m-30) cc_final: 0.8865 (p0)
REVERT: A  514 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6242 (pm20)
REVERT: A  527 TYR cc_start: 0.8321 (t80) cc_final: 0.8000 (t80)
REVERT: B  152 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8759 (t0)
REVERT: B  300 TYR cc_start: 0.5093 (OUTLIER) cc_final: 0.4621 (m-10)
  outliers start: 28
  outliers final: 13
  residues processed: 72
  average time/residue: 0.1668
  time to fit residues: 18.1402
Evaluate side-chains
  61 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
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  514 GLU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  434 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0470
   chunk 29 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 94 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   overall best weight:    2.3882

-------------------------------------------------------------------------------
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 ** 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 = 0.3685 r_free = 0.3685 target = 0.064652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.044251 restraints weight = 42877.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.046331 restraints weight = 22532.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.047653 restraints weight = 15297.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8306  Z= 0.226
  Angle     :  0.650   8.475  11182  Z= 0.335
  Chirality :  0.043   0.157   1222
  Planarity :  0.004   0.049   1426
  Dihedral  :  9.545  79.512   1150
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 28.35 %
    Favored  : 68.19 %
  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: -1.35 (0.27), residues: 986
  helix:  0.10 (0.29), residues: 315
  sheet: -0.10 (0.44), residues: 173
  loop : -1.89 (0.26), residues: 498

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   0.026   0.001   PHE B 498 
 TYR   0.013   0.001   TYR A 428 
 ARG   0.003   0.000   ARG A 455 

*********************** 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
  72 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 41
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7990 (m-80)
REVERT: A   93 MET cc_start: 0.7559 (mmt) cc_final: 0.6383 (mmt)
REVERT: A  117 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8515 (mp)
REVERT: A  267 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6775 (pptt)
REVERT: A  463 ASP cc_start: 0.9171 (m-30) cc_final: 0.8875 (p0)
REVERT: A  514 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6193 (pm20)
REVERT: A  527 TYR cc_start: 0.8298 (t80) cc_final: 0.7939 (t80)
REVERT: B   84 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6400 (t80)
REVERT: B   93 MET cc_start: 0.7512 (mmt) cc_final: 0.6812 (mmt)
REVERT: B  152 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8725 (t70)
REVERT: B  300 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4628 (m-10)
  outliers start: 31
  outliers final: 17
  residues processed: 71
  average time/residue: 0.1801
  time to fit residues: 19.2957
Evaluate side-chains
  64 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 40
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
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  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  125 MET
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  469 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 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 = 0.3653 r_free = 0.3653 target = 0.063342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.043153 restraints weight = 44501.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.045129 restraints weight = 23826.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.046407 restraints weight = 16319.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8306  Z= 0.339
  Angle     :  0.707   9.090  11182  Z= 0.364
  Chirality :  0.044   0.153   1222
  Planarity :  0.004   0.050   1426
  Dihedral  :  9.643  81.578   1150
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 28.57 %
    Favored  : 67.97 %
  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: -1.51 (0.27), residues: 986
  helix: -0.09 (0.29), residues: 313
  sheet: -0.16 (0.44), residues: 168
  loop : -1.94 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 311 
 HIS   0.006   0.002   HIS B 205 
 PHE   0.013   0.002   PHE B 303 
 TYR   0.015   0.002   TYR A 428 
 ARG   0.004   0.001   ARG B 329 

*********************** 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
  70 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 39
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8041 (m-80)
REVERT: A   93 MET cc_start: 0.7934 (mmt) cc_final: 0.6971 (mmt)
REVERT: A  117 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8514 (mp)
REVERT: A  267 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6766 (pptt)
REVERT: A  463 ASP cc_start: 0.9112 (m-30) cc_final: 0.8895 (p0)
REVERT: A  514 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6275 (pm20)
REVERT: A  527 TYR cc_start: 0.8339 (t80) cc_final: 0.7953 (t80)
REVERT: B   84 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6395 (t80)
REVERT: B   93 MET cc_start: 0.7566 (mmt) cc_final: 0.7008 (mmt)
REVERT: B  152 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8702 (t70)
REVERT: B  300 TYR cc_start: 0.5051 (OUTLIER) cc_final: 0.4692 (m-10)
  outliers start: 31
  outliers final: 20
  residues processed: 69
  average time/residue: 0.1679
  time to fit residues: 17.4007
Evaluate side-chains
  66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 39
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  193 LEU
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  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  125 MET
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  469 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.065913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.045245 restraints weight = 42569.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.047454 restraints weight = 21918.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.048829 restraints weight = 14667.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8306  Z= 0.171
  Angle     :  0.631   9.117  11182  Z= 0.322
  Chirality :  0.043   0.144   1222
  Planarity :  0.004   0.052   1426
  Dihedral  :  9.123  84.127   1150
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 29.35 %
    Favored  : 68.08 %
  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: -1.23 (0.27), residues: 986
  helix:  0.27 (0.29), residues: 315
  sheet:  0.07 (0.44), residues: 166
  loop : -1.90 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 157 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.008   0.001   PHE B 498 
 TYR   0.010   0.001   TYR B 300 
 ARG   0.002   0.000   ARG B 501 

********************** 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
  66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 43
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7901 (m-80)
REVERT: A   93 MET cc_start: 0.7199 (mmt) cc_final: 0.6818 (mmp)
REVERT: A  117 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8469 (mp)
REVERT: A  267 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6668 (pptt)
REVERT: A  527 TYR cc_start: 0.8371 (t80) cc_final: 0.7963 (t80)
REVERT: B   93 MET cc_start: 0.7298 (mmt) cc_final: 0.6621 (mmt)
REVERT: B  300 TYR cc_start: 0.4842 (OUTLIER) cc_final: 0.4519 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 66
  average time/residue: 0.1683
  time to fit residues: 17.0435
Evaluate side-chains
  60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  117 LEU
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 B residue   24 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  434 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 83 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 93 optimal weight:   20.0000
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.066898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.046366 restraints weight = 42265.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.048607 restraints weight = 21616.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.050008 restraints weight = 14434.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8306  Z= 0.161
  Angle     :  0.615   9.024  11182  Z= 0.314
  Chirality :  0.042   0.146   1222
  Planarity :  0.003   0.051   1426
  Dihedral  :  8.999  84.146   1150
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 30.25 %
    Favored  : 67.97 %
  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: -1.00 (0.27), residues: 986
  helix:  0.55 (0.30), residues: 306
  sheet:  0.29 (0.44), residues: 166
  loop : -1.82 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 157 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.008   0.001   PHE A 165 
 TYR   0.010   0.001   TYR B 511 
 ARG   0.002   0.000   ARG B 501 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2891.14 seconds
wall clock time: 52 minutes 49.20 seconds (3169.20 seconds total)