Starting phenix.real_space_refine
on Wed Mar 12 13:07:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4x_41903/03_2025/8u4x_41903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4x_41903/03_2025/8u4x_41903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u4x_41903/03_2025/8u4x_41903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4x_41903/03_2025/8u4x_41903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4x_41903/03_2025/8u4x_41903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4x_41903/03_2025/8u4x_41903.cif"
  }
  resolution = 2.81
  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=   0.020
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: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4963      2.51       5
     N    1373      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7873
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3890
          Classifications: {'peptide': 499}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 470}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.24, per 1000 atoms: 1.05
  Number of scatterers: 7873
  At special positions: 0
  Unit cell: (100.521, 80.811, 102.492, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1491      8.00
     N    1373      7.00
     C    4963      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 375 " - pdb=" SG  CYS A 379 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 375 " - pdb=" SG  CYS B 379 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Links applied
    TRANS
      " LEU B  12 " - " VAL B  11 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.96
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1874

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      43.2% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 18
    Processing helix  chain 'A' and resid 49 through 52
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 71 through 83
    Processing helix  chain 'A' and resid 121 through 127
    Processing helix  chain 'A' and resid 128 through 133
      removed outlier: 3.983A  pdb=" N   ARG A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A 133 " --> pdb=" O   TYR A 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 128 through 133'
    Processing helix  chain 'A' and resid 135 through 146
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 205 through 215
      removed outlier: 3.820A  pdb=" N   ARG A 214 " --> pdb=" O   GLU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 264
    Processing helix  chain 'A' and resid 294 through 340
      removed outlier: 4.301A  pdb=" N   GLN A 329 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   THR A 330 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 351
    Processing helix  chain 'A' and resid 352 through 361
      removed outlier: 3.595A  pdb=" N   LEU A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 396
      removed outlier: 3.951A  pdb=" N   ALA A 394 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLY A 395 " --> pdb=" O   TRP A 391 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLY A 396 " --> pdb=" O   MET A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.901A  pdb=" N   VAL A 408 " --> pdb=" O   HIS A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 414
      removed outlier: 3.604A  pdb=" N   GLU A 413 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA A 414 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 414'
    Processing helix  chain 'A' and resid 488 through 516
    Processing helix  chain 'B' and resid 12 through 18
    Processing helix  chain 'B' and resid 49 through 52
    Processing helix  chain 'B' and resid 65 through 69
    Processing helix  chain 'B' and resid 71 through 83
    Processing helix  chain 'B' and resid 121 through 127
    Processing helix  chain 'B' and resid 128 through 133
      removed outlier: 3.984A  pdb=" N   ARG B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR B 133 " --> pdb=" O   TYR B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 133'
    Processing helix  chain 'B' and resid 135 through 146
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 205 through 215
      removed outlier: 3.821A  pdb=" N   ARG B 214 " --> pdb=" O   GLU B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 264
    Processing helix  chain 'B' and resid 294 through 340
      removed outlier: 4.302A  pdb=" N   GLN B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   THR B 330 " --> pdb=" O   THR B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 351
    Processing helix  chain 'B' and resid 352 through 361
      removed outlier: 3.595A  pdb=" N   LEU B 356 " --> pdb=" O   GLN B 352 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 396
      removed outlier: 3.951A  pdb=" N   ALA B 394 " --> pdb=" O   THR B 390 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLY B 395 " --> pdb=" O   TRP B 391 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLY B 396 " --> pdb=" O   MET B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 409
      removed outlier: 3.901A  pdb=" N   VAL B 408 " --> pdb=" O   HIS B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 414
      removed outlier: 3.605A  pdb=" N   GLU B 413 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA B 414 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 410 through 414'
    Processing helix  chain 'B' and resid 488 through 516
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27
      removed outlier: 6.204A  pdb=" N   ILE A  43 " --> pdb=" O   LYS A  37 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   LYS A  37 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LEU A  33 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU A 101 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199
      removed outlier: 3.580A  pdb=" N   GLY A 180 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ILE A 171 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLU A 185 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL A 169 " --> pdb=" O   GLU A 185 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   TRP A 280 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   LEU A 279 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLN A 275 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY A 281 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET A 269 " --> pdb=" O   CYS A 285 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 377
    Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 449
      removed outlier: 3.956A  pdb=" N   GLN A 444 " --> pdb=" O   MET A 480 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27
      removed outlier: 6.204A  pdb=" N   ILE B  43 " --> pdb=" O   LYS B  37 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   LYS B  37 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LEU B  33 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU B 101 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199
      removed outlier: 3.580A  pdb=" N   GLY B 180 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ILE B 171 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU B 185 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL B 169 " --> pdb=" O   GLU B 185 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP B 280 " --> pdb=" O   PHE B 174 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   LEU B 279 " --> pdb=" O   GLN B 275 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   GLN B 275 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY B 281 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET B 269 " --> pdb=" O   CYS B 285 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 377
    Processing sheet with id=AA8, first strand: chain 'B' and resid 444 through 449
      removed outlier: 3.957A  pdb=" N   GLN B 444 " --> pdb=" O   MET B 480 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1182 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: 2.31

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1456
        1.33 -     1.45: 1933
        1.45 -     1.57: 4569
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 8036
  Sorted by residual:
  bond pdb=" C   PRO B 410 "
       pdb=" N   PRO B 411 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.011 8.40e-03 1.42e+04 1.83e+00
  bond pdb=" C   PRO A 410 "
       pdb=" N   PRO A 411 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.011 8.40e-03 1.42e+04 1.81e+00
  bond pdb=" CB  GLU B  98 "
       pdb=" CG  GLU B  98 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.03e+00
  bond pdb=" CB  GLU A  98 "
       pdb=" CG  GLU A  98 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.57e-01
  bond pdb=" CD  GLU A  98 "
       pdb=" OE1 GLU A  98 "
    ideal  model  delta    sigma   weight residual
    1.249  1.232  0.017 1.90e-02 2.77e+03 8.46e-01
  ... (remaining 8031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 10458
        1.11 -     2.22: 312
        2.22 -     3.33: 129
        3.33 -     4.44: 14
        4.44 -     5.55: 14
  Bond angle restraints: 10927
  Sorted by residual:
  angle pdb=" CA  GLU A  98 "
        pdb=" CB  GLU A  98 "
        pdb=" CG  GLU A  98 "
      ideal   model   delta    sigma   weight residual
     114.10  119.65   -5.55 2.00e+00 2.50e-01 7.70e+00
  angle pdb=" CA  GLU B  98 "
        pdb=" CB  GLU B  98 "
        pdb=" CG  GLU B  98 "
      ideal   model   delta    sigma   weight residual
     114.10  119.64   -5.54 2.00e+00 2.50e-01 7.68e+00
  angle pdb=" CA  GLN B 372 "
        pdb=" CB  GLN B 372 "
        pdb=" CG  GLN B 372 "
      ideal   model   delta    sigma   weight residual
     114.10  119.23   -5.13 2.00e+00 2.50e-01 6.59e+00
  angle pdb=" CA  GLN A 372 "
        pdb=" CB  GLN A 372 "
        pdb=" CG  GLN A 372 "
      ideal   model   delta    sigma   weight residual
     114.10  119.18   -5.08 2.00e+00 2.50e-01 6.45e+00
  angle pdb=" C   PRO B 410 "
        pdb=" N   PRO B 411 "
        pdb=" CA  PRO B 411 "
      ideal   model   delta    sigma   weight residual
     120.83  118.40    2.43 1.02e+00 9.61e-01 5.67e+00
  ... (remaining 10922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.64: 4019
       14.64 -    29.29: 542
       29.29 -    43.93: 217
       43.93 -    58.58: 77
       58.58 -    73.22: 37
  Dihedral angle restraints: 4892
    sinusoidal: 1999
      harmonic: 2893
  Sorted by residual:
  dihedral pdb=" CB  CYS A 375 "
           pdb=" SG  CYS A 375 "
           pdb=" SG  CYS A 379 "
           pdb=" CB  CYS A 379 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -58.35  -27.65     1      1.00e+01 1.00e-02 1.10e+01
  dihedral pdb=" CB  CYS B 375 "
           pdb=" SG  CYS B 375 "
           pdb=" SG  CYS B 379 "
           pdb=" CB  CYS B 379 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -58.38  -27.62     1      1.00e+01 1.00e-02 1.09e+01
  dihedral pdb=" CG  ARG B 173 "
           pdb=" CD  ARG B 173 "
           pdb=" NE  ARG B 173 "
           pdb=" CZ  ARG B 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.34  -43.34     2      1.50e+01 4.44e-03 1.00e+01
  ... (remaining 4889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 822
       0.032 -    0.064: 249
       0.064 -    0.095: 83
       0.095 -    0.127: 57
       0.127 -    0.159: 11
  Chirality restraints: 1222
  Sorted by residual:
  chirality pdb=" CB  THR A 390 "
            pdb=" CA  THR A 390 "
            pdb=" OG1 THR A 390 "
            pdb=" CG2 THR A 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CB  THR B 390 "
            pdb=" CA  THR B 390 "
            pdb=" OG1 THR B 390 "
            pdb=" CG2 THR B 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CA  VAL A  97 "
            pdb=" N   VAL A  97 "
            pdb=" C   VAL A  97 "
            pdb=" CB  VAL A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.69e-01
  ... (remaining 1219 not shown)

  Planarity restraints: 1429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 409 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO A 410 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 410 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 410 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 409 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO B 410 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 410 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 410 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 454 "   -0.006 2.00e-02 2.50e+03   1.24e-02 1.53e+00
        pdb=" C   LYS A 454 "    0.021 2.00e-02 2.50e+03
        pdb=" O   LYS A 454 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   PRO A 455 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1426 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1629
        2.79 -     3.32: 7219
        3.32 -     3.84: 13233
        3.84 -     4.37: 15171
        4.37 -     4.90: 26144
  Nonbonded interactions: 63396
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 416 "
            pdb=" OG  SER B 420 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   GLN A 416 "
            pdb=" OG  SER A 420 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OE1 GLU B 118 "
            pdb=" OH  TYR B 292 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OE1 GLU A 118 "
            pdb=" OH  TYR A 292 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OE1 GLU B 116 "
            pdb=" OG  SER B 247 "
     model   vdw
     2.268 3.040
  ... (remaining 63391 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 12 through 516 or resid 900))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.640
  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:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     24.430
  Find NCS groups from input model:        0.320
  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:13.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8036  Z= 0.145
  Angle     :  0.559   5.548  10927  Z= 0.300
  Chirality :  0.042   0.159   1222
  Planarity :  0.004   0.032   1428
  Dihedral  : 17.694  73.223   3009
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 27.43 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.28), residues: 991
  helix:  1.98 (0.27), residues: 370
  sheet: -0.28 (0.37), residues: 194
  loop : -0.21 (0.33), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 287 
 PHE   0.008   0.001   PHE B 493 
 TYR   0.008   0.001   TYR A 172 
 ARG   0.007   0.000   ARG A 509 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 241
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7513 (mtt180)
REVERT: A  265 VAL cc_start: 0.8133 (m) cc_final: 0.7904 (p)
REVERT: B   40 GLU cc_start: 0.6098 (tt0) cc_final: 0.5838 (tt0)
REVERT: B   50 VAL cc_start: 0.7879 (m) cc_final: 0.7583 (t)
REVERT: B  118 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7445 (mt-10)
REVERT: B  138 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.7157 (mtp180)
REVERT: B  206 GLU cc_start: 0.7324 (tp30) cc_final: 0.7042 (tp30)
REVERT: B  231 VAL cc_start: 0.7883 (p) cc_final: 0.7621 (m)
REVERT: B  265 VAL cc_start: 0.7980 (m) cc_final: 0.7731 (p)
REVERT: B  454 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8024 (ttpp)
  outliers start: 18
  outliers final: 10
  residues processed: 253
  average time/residue: 1.3975
  time to fit residues: 371.4808
Evaluate side-chains
  234 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 224
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  456 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.0370
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 374 HIS
A 444 GLN
A 468 GLN
B 306 GLN
B 444 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.139149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126521 restraints weight = 10456.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 1.88
r_work: 0.3603 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8036  Z= 0.258
  Angle     :  0.554   5.218  10927  Z= 0.284
  Chirality :  0.044   0.136   1222
  Planarity :  0.005   0.033   1428
  Dihedral  :  6.452  53.165   1132
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 22.04 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.77 (0.27), residues: 991
  helix:  2.07 (0.26), residues: 374
  sheet: -0.39 (0.36), residues: 202
  loop : -0.41 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 476 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.025   0.002   PHE B 493 
 TYR   0.011   0.001   TYR B 172 
 ARG   0.005   0.001   ARG B 168 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 224
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 GLU cc_start: 0.7866 (tp30) cc_final: 0.7583 (mm-30)
REVERT: A  336 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7789 (mm110)
REVERT: A  504 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7595 (mt-10)
REVERT: B  118 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7735 (mt-10)
REVERT: B  163 MET cc_start: 0.8513 (ptm) cc_final: 0.8202 (ptp)
REVERT: B  187 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7819 (t)
REVERT: B  206 GLU cc_start: 0.7370 (tp30) cc_final: 0.7132 (tp30)
REVERT: B  265 VAL cc_start: 0.8334 (m) cc_final: 0.8080 (p)
REVERT: B  336 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7634 (mm110)
REVERT: B  372 GLN cc_start: 0.7207 (mm110) cc_final: 0.6975 (mp10)
  outliers start: 49
  outliers final: 21
  residues processed: 259
  average time/residue: 1.3597
  time to fit residues: 369.7701
Evaluate side-chains
  242 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 220
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0470
   chunk 42 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 374 HIS
A 444 GLN
A 468 GLN
B  60 GLN
B 241 GLN
B 332 GLN
B 444 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.139838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126457 restraints weight = 10532.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 1.99
r_work: 0.3593 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8036  Z= 0.244
  Angle     :  0.541   5.140  10927  Z= 0.275
  Chirality :  0.043   0.133   1222
  Planarity :  0.005   0.035   1428
  Dihedral  :  6.343  52.821   1123
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 23.33 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.74 (0.27), residues: 991
  helix:  2.09 (0.26), residues: 374
  sheet: -0.43 (0.36), residues: 200
  loop : -0.46 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 476 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.034   0.002   PHE B 493 
 TYR   0.010   0.001   TYR A 172 
 ARG   0.004   0.000   ARG A 173 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 222
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 GLU cc_start: 0.8036 (tp30) cc_final: 0.7779 (mm-30)
REVERT: A  207 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7270 (pt0)
REVERT: A  288 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8243 (mtm180)
REVERT: A  336 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7750 (mm110)
REVERT: A  454 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8057 (ttmm)
REVERT: B  163 MET cc_start: 0.8545 (ptm) cc_final: 0.8182 (ptp)
REVERT: B  187 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7887 (t)
REVERT: B  206 GLU cc_start: 0.7435 (tp30) cc_final: 0.7186 (tp30)
REVERT: B  235 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7562 (mtp180)
REVERT: B  336 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7600 (mm110)
  outliers start: 44
  outliers final: 25
  residues processed: 253
  average time/residue: 1.3610
  time to fit residues: 361.5664
Evaluate side-chains
  245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 217
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  444 GLN
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 374 HIS
A 444 GLN
A 468 GLN
A 510 GLN
B  60 GLN
B 241 GLN
B 444 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.139102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125796 restraints weight = 10439.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.97
r_work: 0.3585 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8036  Z= 0.273
  Angle     :  0.558   5.296  10927  Z= 0.284
  Chirality :  0.043   0.139   1222
  Planarity :  0.005   0.036   1428
  Dihedral  :  6.354  52.604   1122
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 23.33 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.27), residues: 991
  helix:  2.01 (0.26), residues: 375
  sheet: -0.42 (0.36), residues: 200
  loop : -0.45 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 476 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.040   0.002   PHE B 493 
 TYR   0.010   0.001   TYR A 172 
 ARG   0.003   0.000   ARG A 173 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 225
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7741 (mt-10)
REVERT: A  207 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7277 (pt0)
REVERT: A  231 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7691 (p)
REVERT: A  336 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7742 (mm110)
REVERT: B  139 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7725 (ttm)
REVERT: B  187 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7890 (t)
REVERT: B  206 GLU cc_start: 0.7446 (tp30) cc_final: 0.7222 (tp30)
REVERT: B  235 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6570 (mtm180)
  outliers start: 51
  outliers final: 26
  residues processed: 259
  average time/residue: 1.3985
  time to fit residues: 379.8492
Evaluate side-chains
  247 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 216
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0060
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 GLN
A 306 GLN
A 374 HIS
A 444 GLN
A 468 GLN
B 120 GLN
B 241 GLN
B 306 GLN
B 336 GLN
B 444 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.139767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126448 restraints weight = 10502.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.98
r_work: 0.3595 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8036  Z= 0.222
  Angle     :  0.539   5.203  10927  Z= 0.275
  Chirality :  0.043   0.142   1222
  Planarity :  0.005   0.036   1428
  Dihedral  :  6.277  52.759   1122
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 24.38 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.74 (0.27), residues: 991
  helix:  2.06 (0.26), residues: 375
  sheet: -0.40 (0.36), residues: 199
  loop : -0.46 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 476 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.044   0.002   PHE B 493 
 TYR   0.009   0.001   TYR A 172 
 ARG   0.004   0.000   ARG A 509 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 220
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7235 (pt0)
REVERT: A  231 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7669 (p)
REVERT: A  288 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8310 (mtm180)
REVERT: A  336 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7730 (mm110)
REVERT: B   76 GLU cc_start: 0.8047 (tp30) cc_final: 0.7813 (mm-30)
REVERT: B  139 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7737 (ttm)
REVERT: B  187 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7932 (t)
REVERT: B  235 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6557 (mtm180)
REVERT: B  446 VAL cc_start: 0.7835 (t) cc_final: 0.7516 (m)
REVERT: B  493 PHE cc_start: 0.7974 (t80) cc_final: 0.7740 (t80)
  outliers start: 44
  outliers final: 23
  residues processed: 251
  average time/residue: 1.3398
  time to fit residues: 353.1923
Evaluate side-chains
  238 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 210
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  444 GLN
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 374 HIS
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 GLN
A 468 GLN
B  60 GLN
B 444 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.138787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.125773 restraints weight = 10453.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.89
r_work: 0.3592 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8036  Z= 0.285
  Angle     :  0.587   6.123  10927  Z= 0.298
  Chirality :  0.044   0.150   1222
  Planarity :  0.005   0.051   1428
  Dihedral  :  6.371  52.441   1122
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 24.97 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.69 (0.27), residues: 991
  helix:  2.00 (0.26), residues: 375
  sheet: -0.42 (0.36), residues: 200
  loop : -0.46 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 476 
 HIS   0.007   0.001   HIS B  30 
 PHE   0.035   0.002   PHE B 493 
 TYR   0.009   0.001   TYR A 172 
 ARG   0.005   0.000   ARG B 288 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 216
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7751 (mt-10)
REVERT: A  207 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7266 (pt0)
REVERT: A  231 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7684 (p)
REVERT: A  288 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8214 (mtm180)
REVERT: A  336 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7729 (mm110)
REVERT: B  118 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: B  185 GLU cc_start: 0.8075 (tp30) cc_final: 0.7772 (tp30)
REVERT: B  187 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7973 (t)
REVERT: B  235 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6556 (mtm180)
REVERT: B  336 GLN cc_start: 0.7830 (mm110) cc_final: 0.7543 (mm110)
  outliers start: 44
  outliers final: 25
  residues processed: 247
  average time/residue: 1.4775
  time to fit residues: 383.3600
Evaluate side-chains
  243 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 72 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0020
   chunk 69 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0370
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.3866

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
A 444 GLN
A 468 GLN
B  60 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.139740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.126813 restraints weight = 10553.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.91
r_work: 0.3604 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8036  Z= 0.211
  Angle     :  0.558   5.287  10927  Z= 0.284
  Chirality :  0.043   0.149   1222
  Planarity :  0.005   0.051   1428
  Dihedral  :  6.280  52.444   1122
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 26.38 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.73 (0.27), residues: 991
  helix:  2.05 (0.26), residues: 375
  sheet: -0.41 (0.36), residues: 197
  loop : -0.46 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 476 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.047   0.002   PHE B 493 
 TYR   0.009   0.001   TYR A 172 
 ARG   0.009   0.000   ARG A 509 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 217
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7229 (pt0)
REVERT: A  231 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7669 (p)
REVERT: A  288 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8180 (mtm180)
REVERT: A  336 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7710 (mm110)
REVERT: A  372 GLN cc_start: 0.7382 (mp10) cc_final: 0.7056 (mp10)
REVERT: B  118 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7733 (mt-10)
REVERT: B  187 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7955 (t)
REVERT: B  235 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6516 (mtm180)
REVERT: B  336 GLN cc_start: 0.7821 (mm110) cc_final: 0.7518 (mm110)
REVERT: B  493 PHE cc_start: 0.7884 (t80) cc_final: 0.7682 (t80)
  outliers start: 37
  outliers final: 23
  residues processed: 243
  average time/residue: 1.3971
  time to fit residues: 356.2942
Evaluate side-chains
  238 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 211
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0570
   chunk 63 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0070
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 374 HIS
A 444 GLN
A 468 GLN
B  60 GLN
B 144 HIS
B 444 GLN
B 468 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.139886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.127028 restraints weight = 10534.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 1.90
r_work: 0.3612 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8036  Z= 0.210
  Angle     :  0.555   5.744  10927  Z= 0.282
  Chirality :  0.043   0.188   1222
  Planarity :  0.005   0.052   1428
  Dihedral  :  6.202  52.231   1122
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 25.56 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.74 (0.27), residues: 991
  helix:  2.05 (0.26), residues: 375
  sheet: -0.40 (0.36), residues: 199
  loop : -0.45 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 476 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.038   0.002   PHE B 493 
 TYR   0.009   0.001   TYR A 172 
 ARG   0.010   0.000   ARG A 509 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 212
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.7833 (m) cc_final: 0.7520 (t)
REVERT: A  118 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: A  185 GLU cc_start: 0.8007 (tp30) cc_final: 0.7656 (mm-30)
REVERT: A  207 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7215 (pt0)
REVERT: A  231 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7641 (p)
REVERT: A  288 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8189 (mtm180)
REVERT: A  372 GLN cc_start: 0.7435 (mp10) cc_final: 0.7074 (mp10)
REVERT: B  118 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: B  187 SER cc_start: 0.8239 (p) cc_final: 0.7947 (t)
REVERT: B  235 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6576 (mtm180)
REVERT: B  336 GLN cc_start: 0.7810 (mm110) cc_final: 0.7501 (mm110)
REVERT: B  446 VAL cc_start: 0.7772 (t) cc_final: 0.7543 (m)
  outliers start: 41
  outliers final: 26
  residues processed: 240
  average time/residue: 1.4877
  time to fit residues: 374.1070
Evaluate side-chains
  241 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 212
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  444 GLN
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 374 HIS
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 GLN
A 468 GLN
B  60 GLN
B 444 GLN
B 468 GLN
B 510 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.139409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.126061 restraints weight = 10655.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.01
r_work: 0.3584 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8036  Z= 0.274
  Angle     :  0.602   7.480  10927  Z= 0.306
  Chirality :  0.044   0.172   1222
  Planarity :  0.005   0.055   1428
  Dihedral  :  6.324  52.085   1122
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.61 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.65 (0.27), residues: 991
  helix:  1.97 (0.26), residues: 375
  sheet: -0.47 (0.36), residues: 198
  loop : -0.48 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 476 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.047   0.002   PHE B 493 
 TYR   0.009   0.001   TYR A 172 
 ARG   0.009   0.001   ARG A 509 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 217
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.7855 (m) cc_final: 0.7542 (t)
REVERT: A  118 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7753 (mt-10)
REVERT: A  207 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7249 (pt0)
REVERT: A  231 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7672 (p)
REVERT: A  288 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.8194 (mtm180)
REVERT: A  372 GLN cc_start: 0.7450 (mp10) cc_final: 0.7063 (mp10)
REVERT: A  480 MET cc_start: 0.8050 (mmm) cc_final: 0.7807 (mmm)
REVERT: B  118 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7741 (mt-10)
REVERT: B  185 GLU cc_start: 0.8080 (tp30) cc_final: 0.7834 (tp30)
REVERT: B  187 SER cc_start: 0.8269 (p) cc_final: 0.8018 (t)
REVERT: B  235 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6588 (mtm180)
REVERT: B  336 GLN cc_start: 0.7835 (mm110) cc_final: 0.7531 (mm110)
REVERT: B  446 VAL cc_start: 0.7814 (t) cc_final: 0.7579 (m)
  outliers start: 35
  outliers final: 28
  residues processed: 244
  average time/residue: 1.3772
  time to fit residues: 352.6018
Evaluate side-chains
  245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 214
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  444 GLN
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 96 optimal weight:    0.2980
   chunk 93 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0670
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 374 HIS
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 GLN
B  60 GLN
B 302 GLN
B 444 GLN
B 468 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.139525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126278 restraints weight = 10526.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 1.99
r_work: 0.3596 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8036  Z= 0.248
  Angle     :  0.595   7.253  10927  Z= 0.304
  Chirality :  0.044   0.166   1222
  Planarity :  0.005   0.057   1428
  Dihedral  :  6.340  52.220   1122
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 26.49 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.63 (0.27), residues: 991
  helix:  1.94 (0.26), residues: 375
  sheet: -0.44 (0.36), residues: 197
  loop : -0.49 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 476 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.011   0.002   PHE B 493 
 TYR   0.009   0.001   TYR A 172 
 ARG   0.009   0.001   ARG A 509 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 212
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: A  139 MET cc_start: 0.7795 (tmm) cc_final: 0.7405 (tmt)
REVERT: A  207 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7237 (pt0)
REVERT: A  231 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7664 (p)
REVERT: A  288 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8141 (mtm180)
REVERT: A  372 GLN cc_start: 0.7451 (mp10) cc_final: 0.7048 (mp10)
REVERT: A  480 MET cc_start: 0.8041 (mmm) cc_final: 0.7774 (mmm)
REVERT: B  118 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7717 (mt-10)
REVERT: B  185 GLU cc_start: 0.8104 (tp30) cc_final: 0.7751 (tp30)
REVERT: B  187 SER cc_start: 0.8258 (p) cc_final: 0.8021 (t)
REVERT: B  235 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6604 (mtm180)
REVERT: B  336 GLN cc_start: 0.7839 (mm110) cc_final: 0.7529 (mm110)
REVERT: B  446 VAL cc_start: 0.7751 (t) cc_final: 0.7484 (m)
  outliers start: 37
  outliers final: 29
  residues processed: 240
  average time/residue: 1.3529
  time to fit residues: 340.9038
Evaluate side-chains
  242 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  444 GLN
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 TRP
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  278 LYS
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  375 CYS
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  444 GLN
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  476 TRP
Chi-restraints excluded: chain B residue  486 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 47 optimal weight:    0.0050
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 86 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0770
   chunk 90 optimal weight:    0.0980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.2352

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
A 444 GLN
A 496 ASN
B  60 GLN
B 444 GLN
B 468 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.141101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.127762 restraints weight = 10589.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.01
r_work: 0.3613 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8036  Z= 0.187
  Angle     :  0.569   6.982  10927  Z= 0.292
  Chirality :  0.043   0.159   1222
  Planarity :  0.005   0.055   1428
  Dihedral  :  6.231  52.355   1122
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 27.90 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.73 (0.27), residues: 991
  helix:  2.02 (0.26), residues: 375
  sheet: -0.35 (0.37), residues: 196
  loop : -0.47 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 476 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.021   0.001   PHE B 493 
 TYR   0.010   0.001   TYR A 259 
 ARG   0.009   0.000   ARG A 509 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7961.63 seconds
wall clock time: 135 minutes 49.02 seconds (8149.02 seconds total)