Starting phenix.real_space_refine
on Wed Feb 12 14:19:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw5_38731/02_2025/8xw5_38731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw5_38731/02_2025/8xw5_38731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw5_38731/02_2025/8xw5_38731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw5_38731/02_2025/8xw5_38731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw5_38731/02_2025/8xw5_38731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw5_38731/02_2025/8xw5_38731.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.036
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      30      5.16       5
     C    5280      2.51       5
     N    1282      2.21       5
     O    1460      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8052
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4026
          Classifications: {'peptide': 543}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 524}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.88, per 1000 atoms: 0.85
  Number of scatterers: 8052
  At special positions: 0
  Unit cell: (101.652, 73.284, 112.684, 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      30     16.00
     O    1460      8.00
     N    1282      7.00
     C    5280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.81
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      70.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 11
    Processing helix  chain 'A' and resid 11 through 19
      removed outlier: 3.546A  pdb=" N   THR A  15 " --> pdb=" O   THR A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.532A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 51
      removed outlier: 3.761A  pdb=" N   LEU A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 77
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.521A  pdb=" N   LYS A  87 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 114
      removed outlier: 3.638A  pdb=" N   LEU A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A  98 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 132 through 145
      removed outlier: 4.103A  pdb=" N   GLY A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 168
      Proline residue:  A 160  - end of helix
      removed outlier: 3.990A  pdb=" N   VAL A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 180
      removed outlier: 3.566A  pdb=" N   ILE A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A 175 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 186
      removed outlier: 3.647A  pdb=" N   LYS A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 201
      removed outlier: 3.500A  pdb=" N   LEU A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 236
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 301 through 312
      removed outlier: 3.570A  pdb=" N   LEU A 305 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   GLN A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ASP A 310 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 4.047A  pdb=" N   THR A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 353
      removed outlier: 3.648A  pdb=" N   GLU A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 381
      removed outlier: 3.762A  pdb=" N   VAL A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 412
      removed outlier: 3.809A  pdb=" N   THR A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 442
      removed outlier: 4.008A  pdb=" N   LEU A 431 " --> pdb=" O   GLN A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 452
      removed outlier: 3.696A  pdb=" N   GLN A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 479
      Proline residue:  A 468  - end of helix
    Processing helix  chain 'A' and resid 483 through 496
    Processing helix  chain 'A' and resid 497 through 509
      removed outlier: 3.896A  pdb=" N   LEU A 501 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ASN A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 503 " --> pdb=" O   ALA A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 543
      Proline residue:  A 522  - end of helix
      removed outlier: 3.662A  pdb=" N   ILE A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY A 535 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      Proline residue:  A 536  - end of helix
    Processing helix  chain 'B' and resid 2 through 11
    Processing helix  chain 'B' and resid 11 through 19
      removed outlier: 3.546A  pdb=" N   THR B  15 " --> pdb=" O   THR B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 28
      removed outlier: 3.532A  pdb=" N   LEU B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 51
      removed outlier: 3.761A  pdb=" N   LEU B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU B  48 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 77
    Processing helix  chain 'B' and resid 80 through 88
      removed outlier: 3.521A  pdb=" N   LYS B  87 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 114
      removed outlier: 3.638A  pdb=" N   LEU B  97 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B  98 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 132 through 145
      removed outlier: 4.103A  pdb=" N   GLY B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 168
      Proline residue:  B 160  - end of helix
      removed outlier: 3.991A  pdb=" N   VAL B 168 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 180
      removed outlier: 3.566A  pdb=" N   ILE B 172 " --> pdb=" O   VAL B 168 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B 175 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 186
      removed outlier: 3.647A  pdb=" N   LYS B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 201
      removed outlier: 3.500A  pdb=" N   LEU B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 266 through 278
    Processing helix  chain 'B' and resid 301 through 312
      removed outlier: 3.570A  pdb=" N   LEU B 305 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   GLN B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ASP B 310 " --> pdb=" O   LYS B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 331
      removed outlier: 4.047A  pdb=" N   THR B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 353
      removed outlier: 3.648A  pdb=" N   GLU B 348 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 381
      removed outlier: 3.762A  pdb=" N   VAL B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 412
      removed outlier: 3.808A  pdb=" N   THR B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 442
      removed outlier: 4.008A  pdb=" N   LEU B 431 " --> pdb=" O   GLN B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 452
      removed outlier: 3.696A  pdb=" N   GLN B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 479
      Proline residue:  B 468  - end of helix
    Processing helix  chain 'B' and resid 483 through 496
    Processing helix  chain 'B' and resid 497 through 509
      removed outlier: 3.896A  pdb=" N   LEU B 501 " --> pdb=" O   LEU B 497 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASN B 502 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP B 503 " --> pdb=" O   ALA B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 543
      Proline residue:  B 522  - end of helix
      removed outlier: 3.662A  pdb=" N   ILE B 526 " --> pdb=" O   PRO B 522 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY B 535 " --> pdb=" O   LEU B 531 " (cutoff:3.500A)
      Proline residue:  B 536  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31
    Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 245
      removed outlier: 6.449A  pdb=" N   ALA A 262 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU A 245 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL A 260 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR A 216 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A 280 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316
    Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 385
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 245
      removed outlier: 6.449A  pdb=" N   ALA B 262 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU B 245 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL B 260 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR B 216 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU B 280 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 313 through 316
    Processing sheet with id=AA8, first strand: chain 'B' and resid 382 through 385

    527 hydrogen bonds defined for protein.
    1563 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: 2.52

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2504
        1.34 -     1.46: 1307
        1.46 -     1.57: 4329
        1.57 -     1.69: 0
        1.69 -     1.80: 58
  Bond restraints: 8198
  Sorted by residual:
  bond pdb=" N   VAL A 208 "
       pdb=" CA  VAL A 208 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   VAL B 208 "
       pdb=" CA  VAL B 208 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   ILE A 204 "
       pdb=" CA  ILE A 204 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.033 1.23e-02 6.61e+03 7.40e+00
  bond pdb=" N   ILE B 204 "
       pdb=" CA  ILE B 204 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.033 1.23e-02 6.61e+03 7.40e+00
  bond pdb=" N   VAL A 206 "
       pdb=" CA  VAL A 206 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.23e-02 6.61e+03 7.14e+00
  ... (remaining 8193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 10714
        1.13 -     2.25: 316
        2.25 -     3.38: 68
        3.38 -     4.51: 26
        4.51 -     5.63: 12
  Bond angle restraints: 11136
  Sorted by residual:
  angle pdb=" CB  GLU B 281 "
        pdb=" CG  GLU B 281 "
        pdb=" CD  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     112.60  117.52   -4.92 1.70e+00 3.46e-01 8.38e+00
  angle pdb=" CB  GLU A 281 "
        pdb=" CG  GLU A 281 "
        pdb=" CD  GLU A 281 "
      ideal   model   delta    sigma   weight residual
     112.60  117.52   -4.92 1.70e+00 3.46e-01 8.38e+00
  angle pdb=" CA  GLU B 281 "
        pdb=" CB  GLU B 281 "
        pdb=" CG  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     114.10  119.73   -5.63 2.00e+00 2.50e-01 7.93e+00
  angle pdb=" CA  GLU A 281 "
        pdb=" CB  GLU A 281 "
        pdb=" CG  GLU A 281 "
      ideal   model   delta    sigma   weight residual
     114.10  119.70   -5.60 2.00e+00 2.50e-01 7.85e+00
  angle pdb=" CA  VAL B 208 "
        pdb=" C   VAL B 208 "
        pdb=" O   VAL B 208 "
      ideal   model   delta    sigma   weight residual
     121.40  118.32    3.08 1.27e+00 6.20e-01 5.87e+00
  ... (remaining 11131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 4208
       14.85 -    29.71: 448
       29.71 -    44.56: 130
       44.56 -    59.42: 26
       59.42 -    74.27: 20
  Dihedral angle restraints: 4832
    sinusoidal: 1756
      harmonic: 3076
  Sorted by residual:
  dihedral pdb=" CA  ASN A 432 "
           pdb=" CB  ASN A 432 "
           pdb=" CG  ASN A 432 "
           pdb=" OD1 ASN A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -165.73  -74.27     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASN B 432 "
           pdb=" CB  ASN B 432 "
           pdb=" CG  ASN B 432 "
           pdb=" OD1 ASN B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -165.73  -74.27     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  VAL B 520 "
           pdb=" C   VAL B 520 "
           pdb=" N   ALA B 521 "
           pdb=" CA  ALA B 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.51  -15.49     0      5.00e+00 4.00e-02 9.60e+00
  ... (remaining 4829 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1005
       0.040 -    0.080: 281
       0.080 -    0.120: 82
       0.120 -    0.160: 10
       0.160 -    0.200: 4
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CA  VAL B 206 "
            pdb=" N   VAL B 206 "
            pdb=" C   VAL B 206 "
            pdb=" CB  VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CA  VAL A 208 "
            pdb=" N   VAL A 208 "
            pdb=" C   VAL A 208 "
            pdb=" CB  VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.92e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 281 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" CD  GLU A 281 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 281 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 281 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 281 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" CD  GLU B 281 "   -0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 281 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 281 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 324 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 325 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 29
        2.60 -     3.18: 7210
        3.18 -     3.75: 12760
        3.75 -     4.33: 16858
        4.33 -     4.90: 28584
  Nonbonded interactions: 65441
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A  60 "
            pdb=" SG  CYS B  60 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" O   GLU B 140 "
            pdb=" OG  SER B 143 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   GLU A 140 "
            pdb=" OG  SER A 143 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE1 GLN A 227 "
            pdb=" NZ  LYS A 235 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" OE1 GLN B 227 "
            pdb=" NZ  LYS B 235 "
     model   vdw
     2.347 3.120
  ... (remaining 65436 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.890
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.660
  Find NCS groups from input model:        0.150
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
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      :  0.003   0.039   8198  Z= 0.188
  Angle     :  0.526   5.632  11136  Z= 0.296
  Chirality :  0.041   0.200   1382
  Planarity :  0.004   0.030   1378
  Dihedral  : 14.483  74.272   2868
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 16.98 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1082
  helix:  1.07 (0.19), residues: 736
  sheet: -0.40 (0.77), residues: 56
  loop : -0.03 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 367 
 HIS   0.002   0.000   HIS A 414 
 PHE   0.013   0.001   PHE B 111 
 TYR   0.011   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 179 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  112 LYS cc_start: 0.7096 (tttt) cc_final: 0.6679 (tppt)
REVERT: A  227 GLN cc_start: 0.6908 (mt0) cc_final: 0.6407 (mm-40)
REVERT: B  227 GLN cc_start: 0.6555 (mt0) cc_final: 0.6300 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2000
  time to fit residues: 22.9204
Evaluate side-chains
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.184201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150493 restraints weight = 8560.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.154901 restraints weight = 5468.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.157699 restraints weight = 4148.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8198  Z= 0.234
  Angle     :  0.513   6.480  11136  Z= 0.275
  Chirality :  0.041   0.129   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.652  59.363   1130
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 13.84 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1082
  helix:  1.09 (0.19), residues: 742
  sheet: -0.53 (0.79), residues: 56
  loop :  0.01 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 367 
 HIS   0.004   0.001   HIS B 414 
 PHE   0.010   0.001   PHE A  69 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.002   0.001   ARG A 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 89
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7899 (tt)
REVERT: A  112 LYS cc_start: 0.7873 (tttt) cc_final: 0.7581 (tppt)
REVERT: A  203 MET cc_start: 0.7507 (mtt) cc_final: 0.7159 (mtp)
REVERT: A  256 ASN cc_start: 0.6830 (p0) cc_final: 0.6589 (p0)
REVERT: A  281 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: B   20 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8138 (tt)
REVERT: B   85 MET cc_start: 0.8039 (mmp) cc_final: 0.7791 (mmt)
REVERT: B  182 MET cc_start: 0.8375 (tpp) cc_final: 0.8021 (ttt)
REVERT: B  186 MET cc_start: 0.7302 (mtm) cc_final: 0.7007 (mtp)
  outliers start: 37
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1687
  time to fit residues: 28.2221
Evaluate side-chains
  105 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 227 GLN
B 469 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.197669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.167609 restraints weight = 8835.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.168194 restraints weight = 6975.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.170007 restraints weight = 5857.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8198  Z= 0.188
  Angle     :  0.467   5.868  11136  Z= 0.251
  Chirality :  0.039   0.129   1382
  Planarity :  0.004   0.035   1378
  Dihedral  :  4.582  58.961   1130
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 14.65 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.25), residues: 1082
  helix:  1.25 (0.19), residues: 740
  sheet: -0.19 (0.85), residues: 52
  loop : -0.06 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.009   0.001   PHE A 515 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B  76 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8011 (tt)
REVERT: A   64 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7197 (mp)
REVERT: A  112 LYS cc_start: 0.7957 (tttt) cc_final: 0.7676 (tppt)
REVERT: A  182 MET cc_start: 0.7707 (ttt) cc_final: 0.7466 (ttt)
REVERT: A  203 MET cc_start: 0.7467 (mtt) cc_final: 0.7138 (mtp)
REVERT: A  299 ASN cc_start: 0.7456 (m-40) cc_final: 0.7154 (p0)
REVERT: A  321 ASP cc_start: 0.7520 (p0) cc_final: 0.7284 (p0)
REVERT: A  433 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8238 (tp)
REVERT: B   20 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8131 (tt)
REVERT: B  182 MET cc_start: 0.8361 (tpp) cc_final: 0.8114 (ttt)
REVERT: B  186 MET cc_start: 0.7276 (mtm) cc_final: 0.6962 (mtp)
REVERT: B  433 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8145 (tt)
  outliers start: 30
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1636
  time to fit residues: 27.0949
Evaluate side-chains
  104 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 52 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   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 227 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.223585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.195478 restraints weight = 8483.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.198213 restraints weight = 6339.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.200458 restraints weight = 5182.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8198  Z= 0.159
  Angle     :  0.459   5.741  11136  Z= 0.245
  Chirality :  0.039   0.128   1382
  Planarity :  0.004   0.038   1378
  Dihedral  :  4.508  58.822   1130
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.93 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1082
  helix:  1.43 (0.19), residues: 740
  sheet: -0.34 (0.76), residues: 62
  loop : -0.09 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 367 
 HIS   0.002   0.000   HIS A 414 
 PHE   0.008   0.001   PHE A 515 
 TYR   0.012   0.001   TYR B 216 
 ARG   0.003   0.000   ARG B  76 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7911 (tt)
REVERT: A  182 MET cc_start: 0.7629 (ttt) cc_final: 0.7413 (ttt)
REVERT: A  321 ASP cc_start: 0.7398 (p0) cc_final: 0.7192 (p0)
REVERT: A  433 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8302 (tp)
REVERT: B   20 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7878 (tt)
REVERT: B  433 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8167 (tt)
  outliers start: 30
  outliers final: 23
  residues processed: 98
  average time/residue: 0.1621
  time to fit residues: 23.2918
Evaluate side-chains
  98 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.218936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.193807 restraints weight = 8415.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.193374 restraints weight = 6258.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.193469 restraints weight = 5814.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8198  Z= 0.170
  Angle     :  0.459   5.924  11136  Z= 0.245
  Chirality :  0.039   0.128   1382
  Planarity :  0.003   0.034   1378
  Dihedral  :  4.483  59.111   1130
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 16.74 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1082
  helix:  1.43 (0.19), residues: 742
  sheet: -0.24 (0.87), residues: 52
  loop : -0.03 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.002   0.000   HIS B 414 
 PHE   0.008   0.001   PHE B  69 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.001   0.000   ARG A 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7849 (tt)
REVERT: A  235 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7559 (ttpp)
REVERT: A  321 ASP cc_start: 0.7386 (p0) cc_final: 0.7175 (p0)
REVERT: A  433 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: B   20 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7869 (tt)
  outliers start: 33
  outliers final: 20
  residues processed: 102
  average time/residue: 0.1785
  time to fit residues: 26.3387
Evaluate side-chains
  99 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0030
   overall best weight:    0.9594

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.187181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152913 restraints weight = 8625.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.157418 restraints weight = 5610.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160041 restraints weight = 4279.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8198  Z= 0.188
  Angle     :  0.482   6.061  11136  Z= 0.255
  Chirality :  0.040   0.145   1382
  Planarity :  0.003   0.035   1378
  Dihedral  :  4.501  59.706   1130
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.09 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.26), residues: 1082
  helix:  1.42 (0.19), residues: 740
  sheet: -0.67 (0.84), residues: 56
  loop : -0.05 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B  76 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7927 (tt)
REVERT: A  235 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7910 (ptpp)
REVERT: A  321 ASP cc_start: 0.7402 (p0) cc_final: 0.7180 (p0)
REVERT: A  433 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8131 (tp)
REVERT: B   20 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7994 (tt)
  outliers start: 27
  outliers final: 21
  residues processed: 92
  average time/residue: 0.1780
  time to fit residues: 23.7722
Evaluate side-chains
  94 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0980
   chunk 101 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0470
   chunk 1 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 528 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.191304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.156318 restraints weight = 8705.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160975 restraints weight = 5573.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.164005 restraints weight = 4237.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8198  Z= 0.145
  Angle     :  0.451   5.415  11136  Z= 0.239
  Chirality :  0.039   0.135   1382
  Planarity :  0.003   0.034   1378
  Dihedral  :  4.414  58.710   1130
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.79 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1082
  helix:  1.63 (0.19), residues: 742
  sheet: -0.69 (0.84), residues: 56
  loop : -0.05 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 367 
 HIS   0.002   0.001   HIS A 414 
 PHE   0.008   0.001   PHE B  69 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.001   0.000   ARG A 507 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7890 (tt)
REVERT: A   64 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6707 (mp)
REVERT: A  235 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7923 (ptpp)
REVERT: A  321 ASP cc_start: 0.7360 (p0) cc_final: 0.7122 (p0)
REVERT: A  433 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (tt)
REVERT: B   20 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7933 (tt)
REVERT: B  112 LYS cc_start: 0.7819 (tttt) cc_final: 0.7550 (tppt)
  outliers start: 22
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1905
  time to fit residues: 24.6876
Evaluate side-chains
  91 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 105 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.189123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.156844 restraints weight = 8783.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158816 restraints weight = 6401.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.161236 restraints weight = 5015.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8198  Z= 0.172
  Angle     :  0.468   5.882  11136  Z= 0.248
  Chirality :  0.039   0.135   1382
  Planarity :  0.003   0.034   1378
  Dihedral  :  4.432  59.673   1130
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.21 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1082
  helix:  1.57 (0.19), residues: 742
  sheet: -0.69 (0.85), residues: 56
  loop : -0.10 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 367 
 HIS   0.002   0.000   HIS B 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7862 (tt)
REVERT: A   64 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6784 (mp)
REVERT: A  235 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7974 (ptpp)
REVERT: A  321 ASP cc_start: 0.7371 (p0) cc_final: 0.7149 (p0)
REVERT: A  433 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8150 (tt)
REVERT: B   20 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7891 (tt)
REVERT: B  112 LYS cc_start: 0.7859 (tttt) cc_final: 0.7596 (tppt)
REVERT: B  182 MET cc_start: 0.7956 (tpp) cc_final: 0.7737 (ttt)
  outliers start: 24
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1956
  time to fit residues: 25.1650
Evaluate side-chains
  89 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 30 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.190035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.157439 restraints weight = 8830.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159783 restraints weight = 6277.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.161860 restraints weight = 4992.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8198  Z= 0.161
  Angle     :  0.466   6.598  11136  Z= 0.246
  Chirality :  0.039   0.130   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.419  59.351   1130
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.21 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1082
  helix:  1.63 (0.19), residues: 746
  sheet: -0.73 (0.85), residues: 56
  loop : -0.04 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 187 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B 355 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7852 (tt)
REVERT: A   64 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6735 (mp)
REVERT: A  227 GLN cc_start: 0.8000 (mt0) cc_final: 0.7354 (mm-40)
REVERT: A  235 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7905 (ptpp)
REVERT: A  321 ASP cc_start: 0.7381 (p0) cc_final: 0.7154 (p0)
REVERT: A  433 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8139 (tt)
REVERT: B   20 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7887 (tt)
REVERT: B  112 LYS cc_start: 0.7844 (tttt) cc_final: 0.7581 (tppt)
REVERT: B  182 MET cc_start: 0.7846 (tpp) cc_final: 0.7599 (ttt)
  outliers start: 21
  outliers final: 15
  residues processed: 85
  average time/residue: 0.1843
  time to fit residues: 22.5822
Evaluate side-chains
  89 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0020
   chunk 14 optimal weight:    0.4980
   chunk 105 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 528 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.190928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.158825 restraints weight = 8754.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160730 restraints weight = 6383.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.163005 restraints weight = 5048.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8198  Z= 0.150
  Angle     :  0.461   5.864  11136  Z= 0.244
  Chirality :  0.039   0.130   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.376  59.201   1130
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.67 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.26), residues: 1082
  helix:  1.74 (0.19), residues: 746
  sheet: -0.70 (0.85), residues: 56
  loop : -0.18 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.001   HIS A 187 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.001   0.000   ARG A 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7834 (tt)
REVERT: A   64 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6789 (mp)
REVERT: A  227 GLN cc_start: 0.7979 (mt0) cc_final: 0.7462 (mm-40)
REVERT: A  321 ASP cc_start: 0.7371 (p0) cc_final: 0.7151 (p0)
REVERT: A  433 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8163 (tt)
REVERT: B   20 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7889 (tt)
REVERT: B  112 LYS cc_start: 0.7901 (tttt) cc_final: 0.7614 (tppt)
  outliers start: 19
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1764
  time to fit residues: 21.6381
Evaluate side-chains
  88 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 83 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.190719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158243 restraints weight = 8726.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.160572 restraints weight = 6284.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.162452 restraints weight = 4999.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8198  Z= 0.156
  Angle     :  0.465   6.529  11136  Z= 0.244
  Chirality :  0.039   0.130   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.375  59.296   1130
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.79 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 1082
  helix:  1.75 (0.19), residues: 746
  sheet: -0.69 (0.85), residues: 56
  loop : -0.22 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.002   0.000   HIS B 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B 409 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2225.96 seconds
wall clock time: 40 minutes 47.41 seconds (2447.41 seconds total)