Starting phenix.real_space_refine
on Wed Sep 17 08:18:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j17_61070/09_2025/9j17_61070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j17_61070/09_2025/9j17_61070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j17_61070/09_2025/9j17_61070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j17_61070/09_2025/9j17_61070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j17_61070/09_2025/9j17_61070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j17_61070/09_2025/9j17_61070.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.047
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      52      5.16       5
     C    4588      2.51       5
     N    1134      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7052
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3510
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 13, 'TRANS': 458}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'ZEA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.35, per 1000 atoms: 0.33
  Number of scatterers: 7052
  At special positions: 0
  Unit cell: (78.1, 115.5, 78.1, 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      52     16.00
     O    1278      8.00
     N    1134      7.00
     C    4588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  72 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 498.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1680

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      62.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 18
      removed outlier: 3.628A  pdb=" N   HIS A  17 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 39 through 55
    Processing helix  chain 'A' and resid 56 through 67
      removed outlier: 4.000A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
    Processing helix  chain 'A' and resid 95 through 128
      removed outlier: 3.583A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 106 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   GLY A 120 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ALA A 123 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 158 through 179
      removed outlier: 3.588A  pdb=" N   ALA A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 186
    Processing helix  chain 'A' and resid 190 through 208
      removed outlier: 3.787A  pdb=" N   ARG A 194 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LEU A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 264
      removed outlier: 3.724A  pdb=" N   LEU A 254 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 286
    Processing helix  chain 'A' and resid 298 through 310
      removed outlier: 4.695A  pdb=" N   LYS A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
      removed outlier: 4.026A  pdb=" N   GLY A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   TYR A 354 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 387
      removed outlier: 3.650A  pdb=" N   VAL A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 379 " --> pdb=" O   TYR A 375 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   SER A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLY A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ALA A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.769A  pdb=" N   LEU A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 422
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 438 through 451
      removed outlier: 3.885A  pdb=" N   GLY A 451 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.798A  pdb=" N   ILE A 456 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 477
      removed outlier: 3.992A  pdb=" N   THR A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 479 through 494
      removed outlier: 3.960A  pdb=" N   GLY A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY A 489 " --> pdb=" O   ILE A 485 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 18
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 39 through 55
    Processing helix  chain 'B' and resid 56 through 67
      removed outlier: 4.000A  pdb=" N   ALA B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP B  67 " --> pdb=" O   ASN B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 95 through 128
      removed outlier: 3.583A  pdb=" N   VAL B 110 " --> pdb=" O   LYS B 106 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   GLY B 120 " --> pdb=" O   SER B 116 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER B 121 " --> pdb=" O   ALA B 117 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ALA B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA B 128 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 158 through 179
      removed outlier: 3.587A  pdb=" N   ALA B 162 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 190 through 208
      removed outlier: 3.787A  pdb=" N   ARG B 194 " --> pdb=" O   PRO B 190 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 264
      removed outlier: 3.724A  pdb=" N   LEU B 254 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 286
    Processing helix  chain 'B' and resid 298 through 310
      removed outlier: 4.695A  pdb=" N   LYS B 310 " --> pdb=" O   ASN B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 356
      removed outlier: 4.026A  pdb=" N   GLY B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 352 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU B 353 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   TYR B 354 " --> pdb=" O   THR B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 387
      removed outlier: 3.649A  pdb=" N   VAL B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA B 379 " --> pdb=" O   TYR B 375 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   SER B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL B 383 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLY B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ALA B 387 " --> pdb=" O   VAL B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 3.769A  pdb=" N   LEU B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 422
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 438 through 451
      removed outlier: 3.884A  pdb=" N   GLY B 451 " --> pdb=" O   VAL B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.798A  pdb=" N   ILE B 456 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 477
      removed outlier: 3.991A  pdb=" N   THR B 466 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   MET B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
      Proline residue:  B 475  - end of helix
    Processing helix  chain 'B' and resid 479 through 494
      removed outlier: 3.960A  pdb=" N   GLY B 483 " --> pdb=" O   SER B 479 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY B 489 " --> pdb=" O   ILE B 485 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 490 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135
      removed outlier: 4.121A  pdb=" N   ALA A 135 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA A 394 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135
      removed outlier: 4.121A  pdb=" N   ALA B 135 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B 394 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 220

    346 hydrogen bonds defined for protein.
    1002 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: 1.10

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2180
        1.34 -     1.46: 1271
        1.46 -     1.57: 3651
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 7192
  Sorted by residual:
  bond pdb=" C4  ZEA B 601 "
       pdb=" C5  ZEA B 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.457 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C4  ZEA A 601 "
       pdb=" C5  ZEA A 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.456 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C5  ZEA A 601 "
       pdb=" C6  ZEA A 601 "
    ideal  model  delta    sigma   weight residual
    1.410  1.463 -0.053 2.00e-02 2.50e+03 7.02e+00
  bond pdb=" C5  ZEA B 601 "
       pdb=" C6  ZEA B 601 "
    ideal  model  delta    sigma   weight residual
    1.410  1.463 -0.053 2.00e-02 2.50e+03 6.95e+00
  bond pdb=" C8  ZEA A 601 "
       pdb=" N9  ZEA A 601 "
    ideal  model  delta    sigma   weight residual
    1.303  1.354 -0.051 2.00e-02 2.50e+03 6.54e+00
  ... (remaining 7187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.05: 9698
        5.05 -    10.11: 42
       10.11 -    15.16: 8
       15.16 -    20.22: 6
       20.22 -    25.27: 6
  Bond angle restraints: 9760
  Sorted by residual:
  angle pdb=" N   ALA A 145 "
        pdb=" CA  ALA A 145 "
        pdb=" C   ALA A 145 "
      ideal   model   delta    sigma   weight residual
     111.33  134.27  -22.94 1.21e+00 6.83e-01 3.59e+02
  angle pdb=" N   ALA B 145 "
        pdb=" CA  ALA B 145 "
        pdb=" C   ALA B 145 "
      ideal   model   delta    sigma   weight residual
     111.33  134.26  -22.93 1.21e+00 6.83e-01 3.59e+02
  angle pdb=" N   ALA A 231 "
        pdb=" CA  ALA A 231 "
        pdb=" C   ALA A 231 "
      ideal   model   delta    sigma   weight residual
     109.96   84.69   25.27 1.50e+00 4.44e-01 2.84e+02
  angle pdb=" N   ALA B 231 "
        pdb=" CA  ALA B 231 "
        pdb=" C   ALA B 231 "
      ideal   model   delta    sigma   weight residual
     109.96   84.69   25.27 1.50e+00 4.44e-01 2.84e+02
  angle pdb=" N   ILE A 144 "
        pdb=" CA  ILE A 144 "
        pdb=" C   ILE A 144 "
      ideal   model   delta    sigma   weight residual
     111.05  129.95  -18.90 1.25e+00 6.40e-01 2.29e+02
  ... (remaining 9755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 3573
       16.24 -    32.49: 425
       32.49 -    48.73: 138
       48.73 -    64.98: 20
       64.98 -    81.22: 10
  Dihedral angle restraints: 4166
    sinusoidal: 1514
      harmonic: 2652
  Sorted by residual:
  dihedral pdb=" C   ILE B 144 "
           pdb=" N   ILE B 144 "
           pdb=" CA  ILE B 144 "
           pdb=" CB  ILE B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -157.38   35.38     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" C   ILE A 144 "
           pdb=" N   ILE A 144 "
           pdb=" CA  ILE A 144 "
           pdb=" CB  ILE A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -157.38   35.38     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" N   ILE B 144 "
           pdb=" C   ILE B 144 "
           pdb=" CA  ILE B 144 "
           pdb=" CB  ILE B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  156.10  -32.70     0      2.50e+00 1.60e-01 1.71e+02
  ... (remaining 4163 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.296: 1170
       0.296 -    0.592: 2
       0.592 -    0.888: 0
       0.888 -    1.184: 2
       1.184 -    1.480: 2
  Chirality restraints: 1176
  Sorted by residual:
  chirality pdb=" CA  ILE B 144 "
            pdb=" N   ILE B 144 "
            pdb=" C   ILE B 144 "
            pdb=" CB  ILE B 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    0.95    1.48 2.00e-01 2.50e+01 5.47e+01
  chirality pdb=" CA  ILE A 144 "
            pdb=" N   ILE A 144 "
            pdb=" C   ILE A 144 "
            pdb=" CB  ILE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    0.95    1.48 2.00e-01 2.50e+01 5.47e+01
  chirality pdb=" CA  ALA A 145 "
            pdb=" N   ALA A 145 "
            pdb=" C   ALA A 145 "
            pdb=" CB  ALA A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.52    0.96 2.00e-01 2.50e+01 2.32e+01
  ... (remaining 1173 not shown)

  Planarity restraints: 1196
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 439 "    0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO A 440 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 440 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 440 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 439 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO B 440 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 440 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 440 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  67 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" C   ASP B  67 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ASP B  67 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER B  68 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1193 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 8
        1.93 -     2.67: 145
        2.67 -     3.42: 10060
        3.42 -     4.16: 15053
        4.16 -     4.90: 28459
  Nonbonded interactions: 53725
  Sorted by model distance:
  nonbonded pdb=" CH2 TRP A 458 "
            pdb=" CE  MET B 450 "
     model   vdw
     1.191 3.760
  nonbonded pdb=" CE  MET A 450 "
            pdb=" CH2 TRP B 458 "
     model   vdw
     1.194 3.760
  nonbonded pdb=" CZ3 TRP A 458 "
            pdb=" CE  MET B 450 "
     model   vdw
     1.577 3.760
  nonbonded pdb=" CE  MET A 450 "
            pdb=" CZ3 TRP B 458 "
     model   vdw
     1.579 3.760
  nonbonded pdb=" CZ2 TRP A 458 "
            pdb=" CE  MET B 450 "
     model   vdw
     1.815 3.760
  ... (remaining 53720 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: 0.03
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.470
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
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   0.070   7196  Z= 0.169
  Angle     :  1.112  25.275   9768  Z= 0.685
  Chirality :  0.087   1.480   1176
  Planarity :  0.004   0.043   1196
  Dihedral  : 15.664  81.221   2474
  Min Nonbonded Distance : 1.191

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 25.40 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.95 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.27), residues: 936
  helix:  0.54 (0.23), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.98 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 104 
 TYR   0.017   0.001   TYR B  98 
 PHE   0.014   0.001   PHE A 368 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.001   0.000   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7192)
  covalent geometry    : angle       1.11142 ( 9760)
  SS BOND              : bond        0.00268 (    4)
  SS BOND              : angle       1.82478 (    8)
  hydrogen bonds       : bond        0.17791 (  346)
  hydrogen bonds       : angle       4.91709 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 MET cc_start: 0.6159 (mmt) cc_final: 0.5882 (mmt)
REVERT: B  163 MET cc_start: 0.6141 (mmt) cc_final: 0.5834 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 115
  average time/residue: 0.0615
  time to fit residues: 10.6387
Evaluate side-chains
  120 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.172118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141420 restraints weight = 9767.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.72
r_work: 0.3540 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7196  Z= 0.112
  Angle     :  0.555   8.007   9768  Z= 0.292
  Chirality :  0.038   0.125   1176
  Planarity :  0.003   0.043   1196
  Dihedral  :  5.389  45.874   1006
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 24.19 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.28), residues: 936
  helix:  0.88 (0.23), residues: 550
  sheet:  None (None), residues: 0
  loop : -2.91 (0.27), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  36 
 TYR   0.009   0.001   TYR B 159 
 PHE   0.017   0.001   PHE B 468 
 TRP   0.009   0.001   TRP B 458 
 HIS   0.001   0.000   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7192)
  covalent geometry    : angle       0.55368 ( 9760)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       1.28839 (    8)
  hydrogen bonds       : bond        0.03589 (  346)
  hydrogen bonds       : angle       3.55977 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  450 MET cc_start: 0.8376 (ttp) cc_final: 0.8013 (ttt)
REVERT: A  463 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7542 (mm-30)
REVERT: A  492 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8368 (tm)
REVERT: B  450 MET cc_start: 0.8392 (ttp) cc_final: 0.8035 (ttt)
REVERT: B  463 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7602 (mm-30)
REVERT: B  492 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8384 (tm)
  outliers start: 24
  outliers final: 12
  residues processed: 147
  average time/residue: 0.0603
  time to fit residues: 13.4807
Evaluate side-chains
  134 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:   20.0000
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0070
   chunk 90 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0070
   overall best weight:    0.7218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.171669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138302 restraints weight = 10075.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.93
r_work: 0.3504 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7196  Z= 0.116
  Angle     :  0.527   7.417   9768  Z= 0.278
  Chirality :  0.038   0.124   1176
  Planarity :  0.003   0.043   1196
  Dihedral  :  5.355  46.489   1006
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 23.79 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.28), residues: 936
  helix:  1.04 (0.23), residues: 556
  sheet:  None (None), residues: 0
  loop : -2.92 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  36 
 TYR   0.008   0.001   TYR B 375 
 PHE   0.013   0.001   PHE A 468 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.001   0.000   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7192)
  covalent geometry    : angle       0.52596 ( 9760)
  SS BOND              : bond        0.00311 (    4)
  SS BOND              : angle       1.39247 (    8)
  hydrogen bonds       : bond        0.03493 (  346)
  hydrogen bonds       : angle       3.37712 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  463 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7563 (mm-30)
REVERT: A  492 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8307 (tm)
REVERT: B   76 ASP cc_start: 0.8176 (t70) cc_final: 0.7691 (t70)
REVERT: B  463 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7552 (mm-30)
REVERT: B  492 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8318 (tm)
  outliers start: 34
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0586
  time to fit residues: 13.1046
Evaluate side-chains
  142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 20 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.170813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137329 restraints weight = 10242.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.94
r_work: 0.3491 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7196  Z= 0.121
  Angle     :  0.534   6.197   9768  Z= 0.283
  Chirality :  0.038   0.128   1176
  Planarity :  0.004   0.043   1196
  Dihedral  :  5.352  46.265   1006
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.87 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.28), residues: 936
  helix:  1.13 (0.23), residues: 568
  sheet:  None (None), residues: 0
  loop : -2.84 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  36 
 TYR   0.007   0.001   TYR A 375 
 PHE   0.012   0.001   PHE A 468 
 TRP   0.009   0.001   TRP B 458 
 HIS   0.001   0.000   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7192)
  covalent geometry    : angle       0.53212 ( 9760)
  SS BOND              : bond        0.00338 (    4)
  SS BOND              : angle       1.50378 (    8)
  hydrogen bonds       : bond        0.03464 (  346)
  hydrogen bonds       : angle       3.40227 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  463 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7618 (mm-30)
REVERT: A  492 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8333 (tm)
REVERT: B  463 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7583 (mm-30)
REVERT: B  492 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8335 (tm)
  outliers start: 31
  outliers final: 19
  residues processed: 143
  average time/residue: 0.0606
  time to fit residues: 13.2280
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.170348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.137019 restraints weight = 10113.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.92
r_work: 0.3476 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7196  Z= 0.129
  Angle     :  0.563  10.030   9768  Z= 0.293
  Chirality :  0.038   0.125   1176
  Planarity :  0.004   0.045   1196
  Dihedral  :  5.446  47.546   1006
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.81 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.28), residues: 936
  helix:  1.26 (0.23), residues: 558
  sheet:  None (None), residues: 0
  loop : -2.85 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  36 
 TYR   0.008   0.001   TYR A  98 
 PHE   0.011   0.001   PHE A 468 
 TRP   0.008   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7192)
  covalent geometry    : angle       0.56179 ( 9760)
  SS BOND              : bond        0.00360 (    4)
  SS BOND              : angle       1.56666 (    8)
  hydrogen bonds       : bond        0.03538 (  346)
  hydrogen bonds       : angle       3.41431 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8237 (tt)
REVERT: A  463 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7601 (mm-30)
REVERT: A  492 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8354 (tm)
REVERT: B   67 ASP cc_start: 0.8422 (p0) cc_final: 0.8153 (p0)
REVERT: B   76 ASP cc_start: 0.8235 (t70) cc_final: 0.7806 (t70)
REVERT: B  185 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8248 (tt)
REVERT: B  313 ASP cc_start: 0.8916 (t0) cc_final: 0.8695 (t0)
REVERT: B  463 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7602 (mm-30)
REVERT: B  492 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8357 (tm)
  outliers start: 33
  outliers final: 25
  residues processed: 149
  average time/residue: 0.0594
  time to fit residues: 13.3834
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 60 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.168748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137938 restraints weight = 9763.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.71
r_work: 0.3491 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7196  Z= 0.120
  Angle     :  0.548   8.500   9768  Z= 0.286
  Chirality :  0.038   0.123   1176
  Planarity :  0.004   0.047   1196
  Dihedral  :  5.394  47.556   1006
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 25.54 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.28), residues: 936
  helix:  1.26 (0.23), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.81 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  36 
 TYR   0.008   0.001   TYR B  98 
 PHE   0.010   0.001   PHE A 468 
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7192)
  covalent geometry    : angle       0.54627 ( 9760)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       1.60948 (    8)
  hydrogen bonds       : bond        0.03396 (  346)
  hydrogen bonds       : angle       3.36151 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8266 (tt)
REVERT: A  211 GLN cc_start: 0.8663 (mp10) cc_final: 0.8181 (mp10)
REVERT: A  463 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7594 (mm-30)
REVERT: A  492 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8443 (tm)
REVERT: B   67 ASP cc_start: 0.8306 (p0) cc_final: 0.8010 (p0)
REVERT: B  185 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8222 (tt)
REVERT: B  211 GLN cc_start: 0.8663 (mp10) cc_final: 0.8187 (mp10)
REVERT: B  463 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7575 (mm-30)
REVERT: B  492 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8414 (tm)
  outliers start: 35
  outliers final: 26
  residues processed: 147
  average time/residue: 0.0572
  time to fit residues: 12.7062
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    0.2980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 160 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.170662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.137034 restraints weight = 10081.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.93
r_work: 0.3479 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7196  Z= 0.123
  Angle     :  0.554   7.901   9768  Z= 0.291
  Chirality :  0.039   0.143   1176
  Planarity :  0.004   0.050   1196
  Dihedral  :  5.397  48.111   1006
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 25.27 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.28), residues: 936
  helix:  1.23 (0.23), residues: 570
  sheet:  None (None), residues: 0
  loop : -2.84 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 330 
 TYR   0.008   0.001   TYR B  98 
 PHE   0.009   0.001   PHE A 468 
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7192)
  covalent geometry    : angle       0.55262 ( 9760)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       1.63304 (    8)
  hydrogen bonds       : bond        0.03450 (  346)
  hydrogen bonds       : angle       3.37574 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8250 (tt)
REVERT: A  211 GLN cc_start: 0.8670 (mp10) cc_final: 0.8123 (mp10)
REVERT: A  463 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7602 (mm-30)
REVERT: A  492 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8368 (tm)
REVERT: B   67 ASP cc_start: 0.8369 (p0) cc_final: 0.8127 (p0)
REVERT: B   76 ASP cc_start: 0.8303 (t70) cc_final: 0.7802 (t70)
REVERT: B  185 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8273 (tt)
REVERT: B  211 GLN cc_start: 0.8661 (mp10) cc_final: 0.8106 (mp10)
REVERT: B  463 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7601 (mm-30)
REVERT: B  492 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8343 (tm)
  outliers start: 37
  outliers final: 27
  residues processed: 149
  average time/residue: 0.0597
  time to fit residues: 13.5116
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN
B 147 ASN
B 160 HIS
B 482 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.172568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.139217 restraints weight = 10067.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.93
r_work: 0.3510 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7196  Z= 0.108
  Angle     :  0.539   8.737   9768  Z= 0.282
  Chirality :  0.038   0.129   1176
  Planarity :  0.004   0.051   1196
  Dihedral  :  5.313  47.647   1006
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 26.21 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.28), residues: 936
  helix:  1.29 (0.23), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.80 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 330 
 TYR   0.008   0.001   TYR B  98 
 PHE   0.010   0.001   PHE A 368 
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7192)
  covalent geometry    : angle       0.53699 ( 9760)
  SS BOND              : bond        0.00329 (    4)
  SS BOND              : angle       1.53530 (    8)
  hydrogen bonds       : bond        0.03116 (  346)
  hydrogen bonds       : angle       3.29881 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8222 (tt)
REVERT: A  463 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7560 (mm-30)
REVERT: A  492 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (tm)
REVERT: B   67 ASP cc_start: 0.8323 (p0) cc_final: 0.7962 (p0)
REVERT: B   76 ASP cc_start: 0.8303 (t70) cc_final: 0.7900 (t70)
REVERT: B  185 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8178 (tt)
REVERT: B  211 GLN cc_start: 0.8615 (mp10) cc_final: 0.8050 (mp10)
REVERT: B  463 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7560 (mm-30)
REVERT: B  492 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8357 (tm)
  outliers start: 28
  outliers final: 20
  residues processed: 141
  average time/residue: 0.0544
  time to fit residues: 11.7488
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.170892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137288 restraints weight = 9909.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.90
r_work: 0.3485 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7196  Z= 0.127
  Angle     :  0.558   8.794   9768  Z= 0.292
  Chirality :  0.039   0.127   1176
  Planarity :  0.004   0.052   1196
  Dihedral  :  5.432  48.911   1006
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 25.81 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.28), residues: 936
  helix:  1.30 (0.23), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.81 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  36 
 TYR   0.009   0.001   TYR B  98 
 PHE   0.012   0.001   PHE B 368 
 TRP   0.006   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7192)
  covalent geometry    : angle       0.55604 ( 9760)
  SS BOND              : bond        0.00391 (    4)
  SS BOND              : angle       1.83251 (    8)
  hydrogen bonds       : bond        0.03438 (  346)
  hydrogen bonds       : angle       3.34557 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8285 (tt)
REVERT: A  211 GLN cc_start: 0.8661 (mp10) cc_final: 0.7719 (mp10)
REVERT: A  463 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7589 (mm-30)
REVERT: A  492 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8367 (tm)
REVERT: B   67 ASP cc_start: 0.8300 (p0) cc_final: 0.8036 (p0)
REVERT: B   76 ASP cc_start: 0.8358 (t70) cc_final: 0.7977 (t70)
REVERT: B   99 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8192 (mm-30)
REVERT: B  185 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8280 (tt)
REVERT: B  463 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7584 (mm-30)
REVERT: B  492 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8360 (tm)
  outliers start: 30
  outliers final: 22
  residues processed: 150
  average time/residue: 0.0585
  time to fit residues: 13.1805
Evaluate side-chains
  146 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 68 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:   20.0000
   chunk 71 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.165893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.135320 restraints weight = 9816.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.68
r_work: 0.3462 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7196  Z= 0.154
  Angle     :  0.611  10.017   9768  Z= 0.317
  Chirality :  0.040   0.126   1176
  Planarity :  0.004   0.052   1196
  Dihedral  :  5.583  50.405   1006
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 25.54 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.28), residues: 936
  helix:  1.25 (0.23), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.86 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  36 
 TYR   0.009   0.001   TYR A  98 
 PHE   0.011   0.001   PHE B 368 
 TRP   0.007   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7192)
  covalent geometry    : angle       0.60892 ( 9760)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       1.90954 (    8)
  hydrogen bonds       : bond        0.03865 (  346)
  hydrogen bonds       : angle       3.47270 ( 1002)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8262 (tt)
REVERT: A  463 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7491 (mm-30)
REVERT: A  492 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8497 (tm)
REVERT: B  185 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8267 (tt)
REVERT: B  463 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7466 (mm-30)
REVERT: B  492 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8471 (tm)
  outliers start: 31
  outliers final: 25
  residues processed: 147
  average time/residue: 0.0587
  time to fit residues: 13.0274
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.167052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.133795 restraints weight = 10043.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.88
r_work: 0.3447 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7196  Z= 0.162
  Angle     :  0.623   9.304   9768  Z= 0.322
  Chirality :  0.041   0.127   1176
  Planarity :  0.004   0.053   1196
  Dihedral  :  5.653  51.635   1006
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 25.13 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.28), residues: 936
  helix:  1.18 (0.23), residues: 568
  sheet:  None (None), residues: 0
  loop : -2.59 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  36 
 TYR   0.009   0.001   TYR B 372 
 PHE   0.016   0.001   PHE A 368 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 7192)
  covalent geometry    : angle       0.62084 ( 9760)
  SS BOND              : bond        0.00433 (    4)
  SS BOND              : angle       1.95926 (    8)
  hydrogen bonds       : bond        0.03933 (  346)
  hydrogen bonds       : angle       3.48817 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1542.54 seconds
wall clock time: 27 minutes 10.61 seconds (1630.61 seconds total)