Starting phenix.real_space_refine
on Wed Feb 12 08:40:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1r_32947/02_2025/7x1r_32947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1r_32947/02_2025/7x1r_32947.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/7x1r_32947/02_2025/7x1r_32947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1r_32947/02_2025/7x1r_32947.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1r_32947/02_2025/7x1r_32947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1r_32947/02_2025/7x1r_32947.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=   0.001 sd=   0.019
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
     Au      2     10.57       5
     P       4      5.49       5
     S      38      5.16       5
     C    4824      2.51       5
     N    1298      2.21       5
     O    1442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7608
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3750
          Classifications: {'peptide': 485}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {' AU': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1419  SG  CYS A 189      73.629  62.408  61.033  1.00 28.54           S

  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb="AU    AU A 502 " occ=0.30
    residue:
      pdb="AU    AU B 502 " occ=0.30
  Time building chain proxies: 6.35, per 1000 atoms: 0.83
  Number of scatterers: 7608
  At special positions: 0
  Unit cell: (116.8, 104, 76.8, 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)
     Au      2     78.96
     S      38     16.00
     P       4     15.00
     O    1442      8.00
     N    1298      7.00
     C    4824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  64 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      36.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 4.346A  pdb=" N   VAL A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 123
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 184'
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 342 through 359
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 430 through 432
      No H-bonds generated for 'chain 'A' and resid 430 through 432'
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'B' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR B  34 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 4.347A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 123
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE B 184 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 184'
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 229 through 243
    Processing helix  chain 'B' and resid 342 through 359
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 430 through 432
      No H-bonds generated for 'chain 'B' and resid 430 through 432'
    Processing helix  chain 'B' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY B 451 " --> pdb=" O   GLU B 447 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 474 through 481
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ARG A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 135 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR A 330 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   PHE A 157 " --> pdb=" O   TYR A 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.828A  pdb=" N   ILE A 178 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN A 272 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ARG A 266 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL A 435 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN A 428 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ARG B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 135 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR B 330 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   PHE B 157 " --> pdb=" O   TYR B 330 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165
    Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179
      removed outlier: 6.829A  pdb=" N   ILE B 178 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN B 272 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ARG B 266 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL B 435 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN B 428 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    948 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: 2.29

  Time building geometry restraints manager: 2.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2486
        1.35 -     1.47: 1858
        1.47 -     1.60: 3368
        1.60 -     1.72: 0
        1.72 -     1.85: 52
  Bond restraints: 7764
  Sorted by residual:
  bond pdb=" O3P FAD B 501 "
       pdb=" P   FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" O5B FAD B 501 "
       pdb=" PA  FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" O5' FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.573  0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 7759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10120
        1.67 -     3.33: 354
        3.33 -     5.00: 33
        5.00 -     6.66: 21
        6.66 -     8.33: 4
  Bond angle restraints: 10532
  Sorted by residual:
  angle pdb=" N   VAL A 305 "
        pdb=" CA  VAL A 305 "
        pdb=" C   VAL A 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" N   VAL B 305 "
        pdb=" CA  VAL B 305 "
        pdb=" C   VAL B 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" C   GLY A 207 "
        pdb=" N   PHE A 208 "
        pdb=" CA  PHE A 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.43    5.71 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   GLY B 207 "
        pdb=" N   PHE B 208 "
        pdb=" CA  PHE B 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.45    5.69 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   ARG B 221 "
        pdb=" N   SER B 222 "
        pdb=" CA  SER B 222 "
      ideal   model   delta    sigma   weight residual
     122.17  117.21    4.96 1.54e+00 4.22e-01 1.04e+01
  ... (remaining 10527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4240
       17.52 -    35.03: 327
       35.03 -    52.55: 65
       52.55 -    70.06: 16
       70.06 -    87.58: 15
  Dihedral angle restraints: 4663
    sinusoidal: 1909
      harmonic: 2754
  Sorted by residual:
  dihedral pdb=" CA  CYS A  59 "
           pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.60  -74.60     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  ALA B 160 "
           pdb=" C   ALA B 160 "
           pdb=" N   THR B 161 "
           pdb=" CA  THR B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ALA A 160 "
           pdb=" C   ALA A 160 "
           pdb=" N   THR A 161 "
           pdb=" CA  THR A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.00  -18.00     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4660 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 653
       0.034 -    0.068: 317
       0.068 -    0.102: 141
       0.102 -    0.136: 54
       0.136 -    0.169: 9
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  PHE B 208 "
            pdb=" N   PHE B 208 "
            pdb=" C   PHE B 208 "
            pdb=" CB  PHE B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CA  PHE A 208 "
            pdb=" N   PHE A 208 "
            pdb=" C   PHE A 208 "
            pdb=" CB  PHE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" C2B FAD B 501 "
            pdb=" C1B FAD B 501 "
            pdb=" C3B FAD B 501 "
            pdb=" O2B FAD B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.70    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 170 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B 171 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 171 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 171 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 170 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 171 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 171 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 171 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 208 "    0.011 2.00e-02 2.50e+03   9.59e-03 1.61e+00
        pdb=" CG  PHE B 208 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 208 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 208 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 208 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 67
        2.61 -     3.18: 6725
        3.18 -     3.75: 11359
        3.75 -     4.33: 16219
        4.33 -     4.90: 26855
  Nonbonded interactions: 61225
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  59 "
            pdb=" SG  CYS B  64 "
     model   vdw
     2.036 3.760
  nonbonded pdb=" SG  CYS B 189 "
            pdb="AU    AU B 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" SG  CYS A 189 "
            pdb="AU    AU A 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" O   LEU A  55 "
            pdb=" ND2 ASN A 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   LEU B  55 "
            pdb=" ND2 ASN B 113 "
     model   vdw
     2.207 3.120
  ... (remaining 61220 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=0.30 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:             0.040
  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:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.410
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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      :  0.007   0.101   7764  Z= 0.470
  Angle     :  0.755   8.330  10532  Z= 0.413
  Chirality :  0.049   0.169   1174
  Planarity :  0.004   0.032   1336
  Dihedral  : 14.250  87.578   2916
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.02 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.24), residues: 966
  helix:  0.38 (0.27), residues: 290
  sheet: -0.35 (0.32), residues: 264
  loop : -1.43 (0.26), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  53 
 HIS   0.005   0.002   HIS A  71 
 PHE   0.022   0.003   PHE B 208 
 TYR   0.015   0.002   TYR B 200 
 ARG   0.003   0.001   ARG A 434 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9074 (mt) cc_final: 0.8771 (mt)
REVERT: A   30 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6698 (mm-30)
REVERT: A   81 GLN cc_start: 0.8038 (tt0) cc_final: 0.7754 (tt0)
REVERT: A   85 ASN cc_start: 0.8588 (m110) cc_final: 0.8295 (m-40)
REVERT: A  139 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7828 (mtp85)
REVERT: A  140 ILE cc_start: 0.8785 (pt) cc_final: 0.8420 (pt)
REVERT: A  222 SER cc_start: 0.8721 (p) cc_final: 0.8229 (t)
REVERT: A  308 LYS cc_start: 0.7830 (mttp) cc_final: 0.7463 (tttm)
REVERT: A  353 LEU cc_start: 0.9041 (tp) cc_final: 0.8723 (tp)
REVERT: A  396 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: A  397 GLU cc_start: 0.7205 (pt0) cc_final: 0.6688 (mt-10)
REVERT: A  450 GLN cc_start: 0.8877 (tp40) cc_final: 0.8558 (tp-100)
REVERT: B   44 VAL cc_start: 0.8996 (p) cc_final: 0.8793 (m)
REVERT: B   85 ASN cc_start: 0.8554 (m110) cc_final: 0.8342 (m-40)
REVERT: B   93 THR cc_start: 0.8339 (t) cc_final: 0.8067 (p)
REVERT: B  192 LYS cc_start: 0.7898 (tttt) cc_final: 0.7447 (ttmm)
REVERT: B  222 SER cc_start: 0.8527 (p) cc_final: 0.8124 (t)
REVERT: B  252 VAL cc_start: 0.9111 (p) cc_final: 0.8899 (m)
REVERT: B  308 LYS cc_start: 0.7904 (mttp) cc_final: 0.7443 (tttm)
REVERT: B  396 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: B  397 GLU cc_start: 0.7094 (pt0) cc_final: 0.6768 (mt-10)
REVERT: B  425 ILE cc_start: 0.8846 (pt) cc_final: 0.8392 (mt)
REVERT: B  450 GLN cc_start: 0.8890 (tp40) cc_final: 0.8554 (tp-100)
  outliers start: 2
  outliers final: 2
  residues processed: 276
  average time/residue: 0.2392
  time to fit residues: 84.5032
Evaluate side-chains
  187 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue  370 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.1980
   chunk 72 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0030
   chunk 24 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.2394

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
A 472 HIS
B 113 ASN
B 144 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.140963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.122984 restraints weight = 8813.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.124253 restraints weight = 7530.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.125422 restraints weight = 6039.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7764  Z= 0.206
  Angle     :  0.562   5.673  10532  Z= 0.301
  Chirality :  0.046   0.152   1174
  Planarity :  0.004   0.051   1336
  Dihedral  :  6.429  45.804   1148
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.79 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 966
  helix:  1.91 (0.29), residues: 294
  sheet:  0.08 (0.33), residues: 256
  loop : -1.08 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  98 
 HIS   0.006   0.002   HIS B  96 
 PHE   0.026   0.002   PHE B 208 
 TYR   0.014   0.002   TYR B  13 
 ARG   0.005   0.000   ARG B 268 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 206
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9028 (mt) cc_final: 0.8708 (mt)
REVERT: A   44 VAL cc_start: 0.8907 (p) cc_final: 0.8705 (m)
REVERT: A  157 PHE cc_start: 0.8535 (m-80) cc_final: 0.8331 (m-10)
REVERT: A  222 SER cc_start: 0.8684 (p) cc_final: 0.8248 (t)
REVERT: A  308 LYS cc_start: 0.7899 (mttp) cc_final: 0.7464 (tttm)
REVERT: A  397 GLU cc_start: 0.7273 (pt0) cc_final: 0.6703 (mt-10)
REVERT: A  450 GLN cc_start: 0.8711 (tp40) cc_final: 0.8467 (tp-100)
REVERT: A  479 PHE cc_start: 0.8650 (m-80) cc_final: 0.8386 (m-80)
REVERT: B   29 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7633 (mttt)
REVERT: B   44 VAL cc_start: 0.9120 (p) cc_final: 0.8871 (m)
REVERT: B   93 THR cc_start: 0.8422 (t) cc_final: 0.8219 (p)
REVERT: B  139 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7743 (mtp85)
REVERT: B  150 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7891 (mtmt)
REVERT: B  157 PHE cc_start: 0.8459 (m-80) cc_final: 0.8237 (m-10)
REVERT: B  192 LYS cc_start: 0.7923 (tttt) cc_final: 0.7571 (ttmm)
REVERT: B  222 SER cc_start: 0.8481 (p) cc_final: 0.8104 (t)
REVERT: B  252 VAL cc_start: 0.8877 (p) cc_final: 0.8649 (m)
REVERT: B  308 LYS cc_start: 0.7848 (mttp) cc_final: 0.7434 (tttm)
REVERT: B  386 SER cc_start: 0.8668 (t) cc_final: 0.8250 (p)
REVERT: B  450 GLN cc_start: 0.8730 (tp40) cc_final: 0.8363 (tp-100)
  outliers start: 14
  outliers final: 9
  residues processed: 216
  average time/residue: 0.1903
  time to fit residues: 55.7284
Evaluate side-chains
  193 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 184
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   chunk 40 optimal weight:    0.2980
   chunk 62 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0670
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.142799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.124471 restraints weight = 9006.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.126985 restraints weight = 7293.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.127937 restraints weight = 5296.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7764  Z= 0.163
  Angle     :  0.518   5.412  10532  Z= 0.277
  Chirality :  0.045   0.155   1174
  Planarity :  0.004   0.039   1336
  Dihedral  :  6.125  46.066   1148
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 15.91 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.26), residues: 966
  helix:  2.33 (0.30), residues: 294
  sheet:  0.19 (0.32), residues: 256
  loop : -0.88 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 407 
 HIS   0.004   0.001   HIS B  96 
 PHE   0.025   0.002   PHE B 208 
 TYR   0.012   0.001   TYR B  13 
 ARG   0.004   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A  139 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7556 (mtp85)
REVERT: A  222 SER cc_start: 0.8818 (p) cc_final: 0.8406 (t)
REVERT: A  308 LYS cc_start: 0.7939 (mttp) cc_final: 0.7456 (tttm)
REVERT: A  450 GLN cc_start: 0.8718 (tp40) cc_final: 0.8408 (tp-100)
REVERT: A  479 PHE cc_start: 0.8502 (m-80) cc_final: 0.8232 (m-80)
REVERT: B   15 LEU cc_start: 0.9261 (tp) cc_final: 0.8932 (tt)
REVERT: B   44 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8853 (m)
REVERT: B  139 ARG cc_start: 0.8365 (mtm110) cc_final: 0.7700 (mtp85)
REVERT: B  222 SER cc_start: 0.8760 (p) cc_final: 0.8321 (t)
REVERT: B  252 VAL cc_start: 0.8755 (p) cc_final: 0.8479 (m)
REVERT: B  289 LEU cc_start: 0.8830 (mt) cc_final: 0.8485 (mp)
REVERT: B  308 LYS cc_start: 0.7887 (mttp) cc_final: 0.7448 (tttm)
REVERT: B  386 SER cc_start: 0.8683 (t) cc_final: 0.8233 (p)
REVERT: B  417 ASP cc_start: 0.7753 (t70) cc_final: 0.7513 (t70)
REVERT: B  425 ILE cc_start: 0.8480 (pt) cc_final: 0.7906 (mt)
REVERT: B  450 GLN cc_start: 0.8766 (tp40) cc_final: 0.8373 (tp-100)
  outliers start: 25
  outliers final: 19
  residues processed: 223
  average time/residue: 0.1951
  time to fit residues: 58.9326
Evaluate side-chains
  206 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  436 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN
B 129 ASN
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.137530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.118516 restraints weight = 9015.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.120161 restraints weight = 8498.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.121380 restraints weight = 6315.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7764  Z= 0.258
  Angle     :  0.571   5.541  10532  Z= 0.303
  Chirality :  0.046   0.145   1174
  Planarity :  0.004   0.034   1336
  Dihedral  :  6.169  45.956   1148
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 18.30 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.26), residues: 966
  helix:  2.61 (0.31), residues: 282
  sheet:  0.06 (0.31), residues: 260
  loop : -0.82 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  88 
 HIS   0.005   0.002   HIS A 108 
 PHE   0.019   0.002   PHE B 208 
 TYR   0.012   0.001   TYR B  13 
 ARG   0.005   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 189
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   39 MET cc_start: 0.8956 (ppp) cc_final: 0.8270 (ppp)
REVERT: A  139 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7546 (mtp85)
REVERT: A  222 SER cc_start: 0.8925 (p) cc_final: 0.8629 (t)
REVERT: A  257 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6956 (mt-10)
REVERT: A  287 VAL cc_start: 0.9184 (t) cc_final: 0.8958 (m)
REVERT: A  308 LYS cc_start: 0.8058 (mttp) cc_final: 0.7494 (tttm)
REVERT: A  403 HIS cc_start: 0.8707 (p90) cc_final: 0.8247 (p90)
REVERT: A  479 PHE cc_start: 0.8660 (m-80) cc_final: 0.8192 (m-80)
REVERT: B   44 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8745 (m)
REVERT: B  139 ARG cc_start: 0.8049 (mtm110) cc_final: 0.7606 (mtp85)
REVERT: B  163 GLU cc_start: 0.7642 (pt0) cc_final: 0.7380 (pm20)
REVERT: B  222 SER cc_start: 0.8912 (p) cc_final: 0.8543 (t)
REVERT: B  252 VAL cc_start: 0.8727 (p) cc_final: 0.8369 (m)
REVERT: B  287 VAL cc_start: 0.9130 (t) cc_final: 0.8881 (m)
REVERT: B  308 LYS cc_start: 0.8043 (mttp) cc_final: 0.7519 (tttm)
  outliers start: 39
  outliers final: 32
  residues processed: 218
  average time/residue: 0.1907
  time to fit residues: 56.7331
Evaluate side-chains
  213 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 179
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  192 LYS
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.0050
   chunk 90 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0170
   chunk 88 optimal weight:    0.2980
   chunk 81 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.3834

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.142841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.125330 restraints weight = 8856.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.126285 restraints weight = 6962.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.126868 restraints weight = 6152.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7764  Z= 0.154
  Angle     :  0.512   6.746  10532  Z= 0.272
  Chirality :  0.044   0.150   1174
  Planarity :  0.004   0.033   1336
  Dihedral  :  5.804  43.552   1148
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.43 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 966
  helix:  2.68 (0.31), residues: 282
  sheet:  0.58 (0.33), residues: 240
  loop : -0.77 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 407 
 HIS   0.004   0.001   HIS B  96 
 PHE   0.026   0.002   PHE A 208 
 TYR   0.009   0.001   TYR A 358 
 ARG   0.005   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 200
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9199 (mp) cc_final: 0.8815 (mm)
REVERT: A   82 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7379 (t0)
REVERT: A  139 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7537 (mtp85)
REVERT: A  140 ILE cc_start: 0.8179 (pt) cc_final: 0.7948 (pt)
REVERT: A  222 SER cc_start: 0.8976 (p) cc_final: 0.8652 (t)
REVERT: A  257 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6825 (mt-10)
REVERT: A  308 LYS cc_start: 0.8092 (mttp) cc_final: 0.7507 (tttm)
REVERT: A  403 HIS cc_start: 0.8556 (p90) cc_final: 0.8286 (p-80)
REVERT: A  479 PHE cc_start: 0.8528 (m-80) cc_final: 0.8114 (m-80)
REVERT: B   44 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8651 (m)
REVERT: B  139 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7636 (mtp85)
REVERT: B  163 GLU cc_start: 0.7640 (pt0) cc_final: 0.7420 (pm20)
REVERT: B  222 SER cc_start: 0.8963 (p) cc_final: 0.8598 (t)
REVERT: B  254 ILE cc_start: 0.8720 (pt) cc_final: 0.8432 (mm)
REVERT: B  287 VAL cc_start: 0.8995 (t) cc_final: 0.8748 (m)
REVERT: B  308 LYS cc_start: 0.8042 (mttp) cc_final: 0.7487 (tttm)
  outliers start: 30
  outliers final: 19
  residues processed: 219
  average time/residue: 0.1790
  time to fit residues: 54.0420
Evaluate side-chains
  201 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 403 HIS ** 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 = 0.3323 r_free = 0.3323 target = 0.131008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.112107 restraints weight = 9290.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.113006 restraints weight = 9430.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.113904 restraints weight = 7858.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056   7764  Z= 0.520
  Angle     :  0.754   8.169  10532  Z= 0.390
  Chirality :  0.051   0.164   1174
  Planarity :  0.005   0.045   1336
  Dihedral  :  6.908  48.434   1148
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 21.80 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 966
  helix:  2.06 (0.31), residues: 278
  sheet: -0.13 (0.32), residues: 244
  loop : -1.04 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A  98 
 HIS   0.008   0.003   HIS B 472 
 PHE   0.021   0.003   PHE A 184 
 TYR   0.019   0.002   TYR A 402 
 ARG   0.007   0.001   ARG A  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.9024 (ppp) cc_final: 0.8669 (ppp)
REVERT: A   76 LEU cc_start: 0.9316 (mp) cc_final: 0.8955 (mm)
REVERT: A  222 SER cc_start: 0.9107 (p) cc_final: 0.8786 (t)
REVERT: A  308 LYS cc_start: 0.8213 (mttp) cc_final: 0.7650 (tttm)
REVERT: A  425 ILE cc_start: 0.8660 (pt) cc_final: 0.8236 (mt)
REVERT: B   76 LEU cc_start: 0.9339 (mp) cc_final: 0.9064 (mm)
REVERT: B  139 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7714 (mtp85)
REVERT: B  163 GLU cc_start: 0.7814 (pt0) cc_final: 0.7122 (pt0)
REVERT: B  222 SER cc_start: 0.9000 (p) cc_final: 0.8641 (t)
REVERT: B  252 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8415 (m)
REVERT: B  308 LYS cc_start: 0.8223 (mttp) cc_final: 0.7510 (tttm)
REVERT: B  356 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6918 (ttm-80)
  outliers start: 43
  outliers final: 33
  residues processed: 203
  average time/residue: 0.1839
  time to fit residues: 51.4803
Evaluate side-chains
  195 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  192 LYS
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 90 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.3464

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN
A 444 ASN
B 243 HIS
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.136673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.119308 restraints weight = 9018.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.118872 restraints weight = 9375.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.120026 restraints weight = 7985.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7764  Z= 0.208
  Angle     :  0.568  10.540  10532  Z= 0.298
  Chirality :  0.046   0.151   1174
  Planarity :  0.004   0.032   1336
  Dihedral  :  6.126  45.360   1148
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 25.19 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.27), residues: 966
  helix:  2.35 (0.31), residues: 284
  sheet: -0.13 (0.33), residues: 244
  loop : -0.84 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  88 
 HIS   0.007   0.002   HIS B  96 
 PHE   0.026   0.002   PHE A 208 
 TYR   0.012   0.001   TYR B 284 
 ARG   0.007   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A   39 MET cc_start: 0.9045 (ppp) cc_final: 0.8833 (ppp)
REVERT: A   76 LEU cc_start: 0.9214 (mp) cc_final: 0.8917 (mm)
REVERT: A  139 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7724 (mtp85)
REVERT: A  222 SER cc_start: 0.9071 (p) cc_final: 0.8785 (t)
REVERT: A  257 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6735 (mt-10)
REVERT: A  308 LYS cc_start: 0.8094 (mttp) cc_final: 0.7594 (tmtt)
REVERT: A  403 HIS cc_start: 0.8412 (p90) cc_final: 0.8105 (p90)
REVERT: A  479 PHE cc_start: 0.8696 (m-80) cc_final: 0.8189 (m-80)
REVERT: B   76 LEU cc_start: 0.9310 (mp) cc_final: 0.9006 (mm)
REVERT: B  139 ARG cc_start: 0.8374 (mtm110) cc_final: 0.7719 (mtp85)
REVERT: B  163 GLU cc_start: 0.7288 (pt0) cc_final: 0.7068 (pt0)
REVERT: B  222 SER cc_start: 0.9103 (p) cc_final: 0.8809 (t)
REVERT: B  280 ILE cc_start: 0.7369 (pt) cc_final: 0.6849 (tt)
REVERT: B  308 LYS cc_start: 0.8085 (mttp) cc_final: 0.7595 (tmtt)
REVERT: B  447 GLU cc_start: 0.8130 (mp0) cc_final: 0.7779 (mp0)
  outliers start: 28
  outliers final: 22
  residues processed: 207
  average time/residue: 0.1763
  time to fit residues: 50.2475
Evaluate side-chains
  201 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
A 444 ASN
** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.134910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.116737 restraints weight = 9278.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.116278 restraints weight = 9925.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.117578 restraints weight = 8583.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7764  Z= 0.280
  Angle     :  0.608  12.184  10532  Z= 0.318
  Chirality :  0.046   0.156   1174
  Planarity :  0.004   0.047   1336
  Dihedral  :  6.206  45.497   1148
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 24.69 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.27), residues: 966
  helix:  2.31 (0.31), residues: 284
  sheet: -0.12 (0.34), residues: 228
  loop : -0.91 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  88 
 HIS   0.006   0.002   HIS B  96 
 PHE   0.026   0.002   PHE B 208 
 TYR   0.012   0.001   TYR B  13 
 ARG   0.009   0.001   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9307 (mp) cc_final: 0.9048 (mm)
REVERT: A  139 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7739 (mtp85)
REVERT: A  222 SER cc_start: 0.9103 (p) cc_final: 0.8863 (t)
REVERT: A  308 LYS cc_start: 0.8132 (mttp) cc_final: 0.7655 (tmtt)
REVERT: B   76 LEU cc_start: 0.9334 (mp) cc_final: 0.8999 (mm)
REVERT: B  139 ARG cc_start: 0.8372 (mtm110) cc_final: 0.7690 (mtp85)
REVERT: B  150 LYS cc_start: 0.8331 (tptp) cc_final: 0.7740 (mtmt)
REVERT: B  222 SER cc_start: 0.9059 (p) cc_final: 0.8851 (t)
REVERT: B  280 ILE cc_start: 0.7421 (pt) cc_final: 0.6866 (tt)
REVERT: B  308 LYS cc_start: 0.8086 (mttp) cc_final: 0.7605 (tmtt)
REVERT: B  356 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7743 (ttm110)
  outliers start: 35
  outliers final: 31
  residues processed: 213
  average time/residue: 0.1737
  time to fit residues: 51.6404
Evaluate side-chains
  214 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 243 HIS
A 444 ASN
B 243 HIS
** B 403 HIS ** 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 = 0.3396 r_free = 0.3396 target = 0.137030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.119271 restraints weight = 9157.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.119484 restraints weight = 9080.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.120465 restraints weight = 7676.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7764  Z= 0.215
  Angle     :  0.589  11.961  10532  Z= 0.308
  Chirality :  0.045   0.157   1174
  Planarity :  0.004   0.050   1336
  Dihedral  :  6.094  46.789   1148
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 26.69 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.27), residues: 966
  helix:  2.39 (0.31), residues: 282
  sheet: -0.25 (0.33), residues: 244
  loop : -0.84 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  88 
 HIS   0.006   0.001   HIS B  96 
 PHE   0.028   0.002   PHE B 208 
 TYR   0.013   0.001   TYR B  13 
 ARG   0.011   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   39 MET cc_start: 0.8919 (ppp) cc_final: 0.8172 (ppp)
REVERT: A   76 LEU cc_start: 0.9243 (mp) cc_final: 0.8969 (mm)
REVERT: A   86 TYR cc_start: 0.8889 (m-80) cc_final: 0.8529 (m-80)
REVERT: A  139 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7709 (mtp85)
REVERT: A  150 LYS cc_start: 0.8297 (tptp) cc_final: 0.7826 (mtmt)
REVERT: A  222 SER cc_start: 0.9088 (p) cc_final: 0.8853 (t)
REVERT: A  257 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6644 (mt-10)
REVERT: A  308 LYS cc_start: 0.8123 (mttp) cc_final: 0.7621 (tmtt)
REVERT: A  366 ASP cc_start: 0.7230 (t0) cc_final: 0.6981 (t0)
REVERT: A  479 PHE cc_start: 0.8660 (m-80) cc_final: 0.8392 (m-80)
REVERT: B   76 LEU cc_start: 0.9294 (mp) cc_final: 0.8935 (mm)
REVERT: B  139 ARG cc_start: 0.8331 (mtm110) cc_final: 0.7690 (mtp85)
REVERT: B  150 LYS cc_start: 0.8301 (tptp) cc_final: 0.7755 (mtmt)
REVERT: B  222 SER cc_start: 0.9055 (p) cc_final: 0.8845 (t)
REVERT: B  280 ILE cc_start: 0.7346 (pt) cc_final: 0.6765 (tt)
REVERT: B  308 LYS cc_start: 0.8086 (mttp) cc_final: 0.7583 (tmtt)
REVERT: B  386 SER cc_start: 0.8672 (t) cc_final: 0.8344 (p)
  outliers start: 27
  outliers final: 25
  residues processed: 209
  average time/residue: 0.2007
  time to fit residues: 59.3723
Evaluate side-chains
  210 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 184
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 25 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.132275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.113621 restraints weight = 9395.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.113253 restraints weight = 9047.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.113970 restraints weight = 9098.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   7764  Z= 0.421
  Angle     :  0.713  13.484  10532  Z= 0.371
  Chirality :  0.049   0.167   1174
  Planarity :  0.005   0.069   1336
  Dihedral  :  6.574  48.219   1147
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 25.69 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.27), residues: 966
  helix:  2.05 (0.31), residues: 282
  sheet: -0.33 (0.35), residues: 228
  loop : -1.01 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  88 
 HIS   0.008   0.002   HIS A 403 
 PHE   0.020   0.002   PHE B 208 
 TYR   0.013   0.002   TYR B  13 
 ARG   0.013   0.001   ARG A  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A   39 MET cc_start: 0.8922 (ppp) cc_final: 0.8581 (ppp)
REVERT: A   64 CYS cc_start: 0.6754 (m) cc_final: 0.6410 (m)
REVERT: A   76 LEU cc_start: 0.9334 (mp) cc_final: 0.9047 (mm)
REVERT: A  139 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7738 (mtp85)
REVERT: A  149 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6334 (tm-30)
REVERT: A  150 LYS cc_start: 0.8336 (tptp) cc_final: 0.7514 (mtmt)
REVERT: A  222 SER cc_start: 0.9150 (p) cc_final: 0.8875 (t)
REVERT: A  257 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6596 (mt-10)
REVERT: A  308 LYS cc_start: 0.8140 (mttp) cc_final: 0.7744 (tmtt)
REVERT: A  366 ASP cc_start: 0.7333 (t0) cc_final: 0.7026 (t0)
REVERT: A  425 ILE cc_start: 0.8704 (pt) cc_final: 0.8288 (mt)
REVERT: B   76 LEU cc_start: 0.9332 (mp) cc_final: 0.9035 (mm)
REVERT: B  103 GLU cc_start: 0.8347 (tp30) cc_final: 0.8032 (tp30)
REVERT: B  139 ARG cc_start: 0.8395 (mtm110) cc_final: 0.7691 (mtp85)
REVERT: B  150 LYS cc_start: 0.8285 (tptp) cc_final: 0.7780 (mtmt)
REVERT: B  222 SER cc_start: 0.9100 (p) cc_final: 0.8865 (t)
REVERT: B  280 ILE cc_start: 0.7515 (pt) cc_final: 0.6912 (tt)
REVERT: B  308 LYS cc_start: 0.8112 (mttp) cc_final: 0.7741 (tmtt)
REVERT: B  386 SER cc_start: 0.8696 (t) cc_final: 0.8448 (p)
REVERT: B  425 ILE cc_start: 0.8685 (pt) cc_final: 0.8349 (mt)
  outliers start: 36
  outliers final: 28
  residues processed: 206
  average time/residue: 0.1744
  time to fit residues: 50.1126
Evaluate side-chains
  212 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ARG
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  475 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 92 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 444 ASN
B 243 HIS
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.137752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.119490 restraints weight = 9017.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.119776 restraints weight = 8821.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.120694 restraints weight = 7316.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7764  Z= 0.204
  Angle     :  0.605  11.839  10532  Z= 0.318
  Chirality :  0.046   0.167   1174
  Planarity :  0.004   0.058   1336
  Dihedral  :  6.143  47.330   1147
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 26.44 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 966
  helix:  2.29 (0.31), residues: 284
  sheet: -0.30 (0.34), residues: 240
  loop : -0.95 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 407 
 HIS   0.010   0.002   HIS B 243 
 PHE   0.031   0.002   PHE B 208 
 TYR   0.012   0.001   TYR B  13 
 ARG   0.012   0.001   ARG B  84 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2412.32 seconds
wall clock time: 44 minutes 6.04 seconds (2646.04 seconds total)