Starting phenix.real_space_refine
on Wed Feb  4 08:42:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mid_23847/02_2026/7mid_23847.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mid_23847/02_2026/7mid_23847.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mid_23847/02_2026/7mid_23847.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mid_23847/02_2026/7mid_23847.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mid_23847/02_2026/7mid_23847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mid_23847/02_2026/7mid_23847.map"
  }
  resolution = 3.56
  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=   0.027
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: 7
    Type Number    sf(0)   Gaussians
     Mn      5      7.51       5
     Fe      4      7.16       5
     P      57      5.49       5
     S      55      5.16       5
     C    5994      2.51       5
     N    1799      2.21       5
     O    1875      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9789
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 4355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4355
          Classifications: {'peptide': 554}
          Link IDs: {'PTRANS': 35, 'TRANS': 518}
    Chain: "B"
      Number of atoms: 2711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2711
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 18, 'TRANS': 321}
    Chain: "C"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 786
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "D"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 758
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 488
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "F"
      Number of atoms: 678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 678
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 9
          Unusual residues: {' MN': 1, 'SF4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    142  SG  CYS A  22      67.781  52.551  83.007  1.00 50.21           S
  ATOM   1468  SG  CYS A 196      64.162  56.883  83.234  1.00 54.73           S
  ATOM   1429  SG  CYS A 190      63.083  53.528  78.591  1.00 55.03           S
  ATOM   1405  SG  CYS A 187      67.882  56.088  79.078  1.00 56.92           S

  Time building chain proxies: 2.17, per 1000 atoms: 0.22
  Number of scatterers: 9789
  At special positions: 0
  Unit cell: (89.8242, 114.062, 135.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     Mn      5     24.99
     S      55     16.00
     P      57     15.00
     O    1875      8.00
     N    1799      7.00
     C    5994      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 395.5 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A 601 "
        pdb="FE4  SF4 A 601 " - pdb=" SG  CYS A 187 "
        pdb="FE3  SF4 A 601 " - pdb=" SG  CYS A 190 "
        pdb="FE2  SF4 A 601 " - pdb=" SG  CYS A 196 "
        pdb="FE1  SF4 A 601 " - pdb=" SG  CYS A  22 "
      Number of angles added : 12


  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 11 sheets defined
      48.3% alpha, 15.3% beta
      16 base pairs and 39 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 20
      removed outlier: 3.564A  pdb=" N   VAL A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 32
    Processing helix  chain 'A' and resid 38 through 53
      removed outlier: 3.895A  pdb=" N   ARG A  50 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL A  51 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 131
    Processing helix  chain 'A' and resid 154 through 175
      removed outlier: 3.816A  pdb=" N   GLY A 175 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 190
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 197 through 205
    Processing helix  chain 'A' and resid 253 through 255
      No H-bonds generated for 'chain 'A' and resid 253 through 255'
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.681A  pdb=" N   ARG A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 315
    Processing helix  chain 'A' and resid 316 through 342
    Processing helix  chain 'A' and resid 353 through 369
    Processing helix  chain 'A' and resid 372 through 390
    Processing helix  chain 'A' and resid 391 through 395
      removed outlier: 3.970A  pdb=" N   LEU A 395 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 4.021A  pdb=" N   ARG A 410 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 440
      removed outlier: 4.066A  pdb=" N   ARG A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLU A 433 " --> pdb=" O   MET A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 465
    Processing helix  chain 'A' and resid 467 through 483
      removed outlier: 4.546A  pdb=" N   LEU A 471 " --> pdb=" O   PRO A 467 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ASP A 474 " --> pdb=" O   PRO A 470 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   SER A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 3.512A  pdb=" N   ARG A 507 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 547
      removed outlier: 3.551A  pdb=" N   GLU A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 279
    Processing helix  chain 'B' and resid 300 through 315
      removed outlier: 4.630A  pdb=" N   VAL B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU B 305 " --> pdb=" O   HIS B 301 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   THR B 306 " --> pdb=" O   ARG B 302 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE B 315 " --> pdb=" O   TYR B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 343
    Processing helix  chain 'B' and resid 353 through 369
    Processing helix  chain 'B' and resid 372 through 390
      removed outlier: 3.921A  pdb=" N   HIS B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 395
    Processing helix  chain 'B' and resid 417 through 441
      removed outlier: 3.536A  pdb=" N   VAL B 441 " --> pdb=" O   ALA B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 473
      removed outlier: 4.182A  pdb=" N   GLU B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      Proline residue:  B 467  - end of helix
      Proline residue:  B 470  - end of helix
    Processing helix  chain 'B' and resid 473 through 483
    Processing helix  chain 'B' and resid 487 through 489
      No H-bonds generated for 'chain 'B' and resid 487 through 489'
    Processing helix  chain 'B' and resid 501 through 517
    Processing helix  chain 'B' and resid 531 through 546
      removed outlier: 4.196A  pdb=" N   GLU B 536 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 28
    Processing helix  chain 'C' and resid 41 through 52
    Processing helix  chain 'C' and resid 74 through 76
      No H-bonds generated for 'chain 'C' and resid 74 through 76'
    Processing helix  chain 'D' and resid 13 through 28
    Processing helix  chain 'D' and resid 41 through 52
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.191A  pdb=" N   ILE A  11 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   LYS A  85 " --> pdb=" O   ILE A  11 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   THR A  83 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   SER A  76 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LYS A  85 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   SER A  74 " --> pdb=" O   LYS A  85 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP A  87 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.191A  pdb=" N   ILE A  11 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   LYS A  85 " --> pdb=" O   ILE A  11 " (cutoff:3.500A)
      removed outlier: 10.683A  pdb=" N   ILE A  86 " --> pdb=" O   TYR A 101 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   TYR A 101 " --> pdb=" O   ILE A  86 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   TYR A 141 " --> pdb=" O   PRO A  98 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ASP A 100 " --> pdb=" O   TYR A 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 226
      removed outlier: 7.191A  pdb=" N   LEU A 222 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA A 261 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU A 224 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   PHE A 263 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL A 226 " --> pdb=" O   PHE A 263 " (cutoff:3.500A)
      removed outlier: 8.848A  pdb=" N   THR A 284 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL A 260 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   LEU A 286 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LEU A 262 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY B 294 " --> pdb=" O   TRP B 285 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   THR B 284 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   VAL B 260 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   LEU B 262 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LEU B 222 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   ALA B 261 " --> pdb=" O   LEU B 222 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   LEU B 224 " --> pdb=" O   ALA B 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 251
      removed outlier: 5.558A  pdb=" N   ARG A 248 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLU A 244 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   CYS A 239 " --> pdb=" O   ASP A 236 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP A 236 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 493
    Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521
    Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251
      removed outlier: 6.854A  pdb=" N   ILE B 242 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   GLU B 251 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU B 240 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 493
    Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 520
    Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.502A  pdb=" N   VAL C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU C   4 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 78 through 80
      removed outlier: 6.764A  pdb=" N   LEU D   4 " --> pdb=" O   LEU D  68 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   VAL D  35 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      43 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      39 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.42: 4387
        1.42 -     1.64: 5639
        1.64 -     1.85: 85
        1.85 -     2.06: 0
        2.06 -     2.28: 12
  Bond restraints: 10123
  Sorted by residual:
  bond pdb=" C1'  DG F  23 "
       pdb=" N9   DG F  23 "
    ideal  model  delta    sigma   weight residual
    1.460  1.357  0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" C1'  DA F  21 "
       pdb=" N9   DA F  21 "
    ideal  model  delta    sigma   weight residual
    1.460  1.377  0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" O3'  DC E   1 "
       pdb=" P    DA E   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.09e+01
  bond pdb=" CA  HIS B 301 "
       pdb=" C   HIS B 301 "
    ideal  model  delta    sigma   weight residual
    1.523  1.467  0.056 1.80e-02 3.09e+03 9.70e+00
  bond pdb=" O3'  DT E  21 "
       pdb=" P    DA E  22 "
    ideal  model  delta    sigma   weight residual
    1.607  1.652 -0.045 1.50e-02 4.44e+03 9.07e+00
  ... (remaining 10118 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.78: 13820
        3.78 -     7.55: 98
        7.55 -    11.33: 18
       11.33 -    15.11: 6
       15.11 -    18.89: 4
  Bond angle restraints: 13946
  Sorted by residual:
  angle pdb=" CD  ARG A 146 "
        pdb=" NE  ARG A 146 "
        pdb=" CZ  ARG A 146 "
      ideal   model   delta    sigma   weight residual
     124.40  138.27  -13.87 1.40e+00 5.10e-01 9.81e+01
  angle pdb=" CG  ARG B 386 "
        pdb=" CD  ARG B 386 "
        pdb=" NE  ARG B 386 "
      ideal   model   delta    sigma   weight residual
     112.00  130.89  -18.89 2.20e+00 2.07e-01 7.37e+01
  angle pdb=" C4'  DA E  22 "
        pdb=" O4'  DA E  22 "
        pdb=" C1'  DA E  22 "
      ideal   model   delta    sigma   weight residual
     109.70   97.14   12.56 1.50e+00 4.44e-01 7.01e+01
  angle pdb=" CA  LYS C  22 "
        pdb=" CB  LYS C  22 "
        pdb=" CG  LYS C  22 "
      ideal   model   delta    sigma   weight residual
     114.10  129.60  -15.50 2.00e+00 2.50e-01 6.01e+01
  angle pdb=" CA  LYS D  22 "
        pdb=" CB  LYS D  22 "
        pdb=" CG  LYS D  22 "
      ideal   model   delta    sigma   weight residual
     114.10  129.55  -15.45 2.00e+00 2.50e-01 5.97e+01
  ... (remaining 13941 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.46: 5346
       28.46 -    56.92: 504
       56.92 -    85.38: 67
       85.38 -   113.84: 3
      113.84 -   142.30: 2
  Dihedral angle restraints: 5922
    sinusoidal: 2822
      harmonic: 3100
  Sorted by residual:
  dihedral pdb=" CD  ARG A 146 "
           pdb=" NE  ARG A 146 "
           pdb=" CZ  ARG A 146 "
           pdb=" NH1 ARG A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -57.87   57.87     1      1.00e+01 1.00e-02 4.49e+01
  dihedral pdb=" CA  ARG A 412 "
           pdb=" C   ARG A 412 "
           pdb=" N   ARG A 413 "
           pdb=" CA  ARG A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.79  -32.21     0      5.00e+00 4.00e-02 4.15e+01
  dihedral pdb=" CA  ARG A 393 "
           pdb=" C   ARG A 393 "
           pdb=" N   MET A 394 "
           pdb=" CA  MET A 394 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.33  -29.67     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 5919 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1353
       0.088 -    0.176: 155
       0.176 -    0.265: 5
       0.265 -    0.353: 1
       0.353 -    0.441: 2
  Chirality restraints: 1516
  Sorted by residual:
  chirality pdb=" C3'  DA E  22 "
            pdb=" C4'  DA E  22 "
            pdb=" O3'  DA E  22 "
            pdb=" C2'  DA E  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.22   -0.44 2.00e-01 2.50e+01 4.86e+00
  chirality pdb=" C4'  DA E  22 "
            pdb=" C5'  DA E  22 "
            pdb=" O4'  DA E  22 "
            pdb=" C3'  DA E  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.11   -0.42 2.00e-01 2.50e+01 4.35e+00
  chirality pdb=" CA  ARG A 146 "
            pdb=" N   ARG A 146 "
            pdb=" C   ARG A 146 "
            pdb=" CB  ARG A 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 1513 not shown)

  Planarity restraints: 1618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 146 "   -0.412 9.50e-02 1.11e+02   1.97e-01 7.98e+01
        pdb=" NE  ARG A 146 "    0.072 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 146 "   -0.128 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 146 "    0.044 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 146 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA E  22 "    0.031 2.00e-02 2.50e+03   1.64e-02 7.43e+00
        pdb=" N9   DA E  22 "   -0.044 2.00e-02 2.50e+03
        pdb=" C8   DA E  22 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA E  22 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA E  22 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DA E  22 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA E  22 "    0.004 2.00e-02 2.50e+03
        pdb=" N1   DA E  22 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DA E  22 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA E  22 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DA E  22 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 316 "    0.043 5.00e-02 4.00e+02   6.63e-02 7.03e+00
        pdb=" N   PRO B 317 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 317 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 317 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1615 not shown)

  Histogram of nonbonded interaction distances:
        0.92 -     1.71: 8
        1.71 -     2.51: 117
        2.51 -     3.31: 11314
        3.31 -     4.10: 24455
        4.10 -     4.90: 45303
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 81197
  Sorted by model distance:
  nonbonded pdb=" N3   DC E  23 "
            pdb=" O6   DG F   4 "
     model   vdw
     0.918 2.496
  nonbonded pdb=" N1   DG E  24 "
            pdb=" N4   DC F   3 "
     model   vdw
     0.939 2.560
  nonbonded pdb=" N2   DG E  24 "
            pdb=" N3   DC F   3 "
     model   vdw
     1.029 2.560
  nonbonded pdb=" CD2 TYR B 232 "
            pdb=" N1   DA E   2 "
     model   vdw
     1.049 3.420
  nonbonded pdb=" CG  TYR B 232 "
            pdb=" C2   DA E   2 "
     model   vdw
     1.295 3.560
  ... (remaining 81192 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 1 through 91 or resid 101))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.210
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
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      :  0.010   0.169  10127  Z= 0.426
  Angle     :  1.376  62.387  13958  Z= 0.579
  Chirality :  0.057   0.441   1516
  Planarity :  0.008   0.197   1618
  Dihedral  : 20.373 142.304   3934
  Min Nonbonded Distance : 0.918

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.58 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  :  1.98 %
    Favored  : 92.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 are not related in a simple way.
  whole: -1.30 (0.26), residues: 1072
  helix:  0.17 (0.23), residues: 493
  sheet: -0.70 (0.47), residues: 138
  loop : -2.10 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.133   0.002   ARG A 146 
 TYR   0.019   0.002   TYR B 545 
 PHE   0.022   0.002   PHE B 425 
 TRP   0.014   0.002   TRP D  30 
 HIS   0.011   0.002   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00952 (10123)
  covalent geometry    : angle       1.01798 (13946)
  hydrogen bonds       : bond        0.16006 (  463)
  hydrogen bonds       : angle       8.15015 ( 1289)
  metal coordination   : bond        0.09359 (    4)
  metal coordination   : angle      31.58409 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 312
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 VAL cc_start: 0.8895 (t) cc_final: 0.8609 (t)
REVERT: A  335 CYS cc_start: 0.4387 (m) cc_final: 0.4113 (m)
REVERT: A  516 MET cc_start: 0.8354 (mmm) cc_final: 0.8126 (mmm)
REVERT: B  432 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7451 (mtt180)
REVERT: B  479 MET cc_start: 0.7090 (mmp) cc_final: 0.6646 (mmt)
REVERT: B  509 ILE cc_start: 0.8087 (mt) cc_final: 0.7717 (mm)
  outliers start: 52
  outliers final: 9
  residues processed: 339
  average time/residue: 0.1300
  time to fit residues: 55.5796
Evaluate side-chains
  173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  341 ARG
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain C residue   94 ILE
Chi-restraints excluded: chain D residue   22 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 206 HIS
A 227 GLN
A 334 ASN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 GLN
B 274 HIS
** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.105199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.089868 restraints weight = 38346.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.092292 restraints weight = 21318.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.093938 restraints weight = 14145.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.094982 restraints weight = 10558.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.095839 restraints weight = 8634.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10127  Z= 0.186
  Angle     :  0.973  44.974  13958  Z= 0.409
  Chirality :  0.046   0.169   1516
  Planarity :  0.006   0.077   1618
  Dihedral  : 20.112 140.247   1862
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.16 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.22 %
    Favored  : 82.25 %
  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 are not related in a simple way.
  whole: -0.89 (0.26), residues: 1072
  helix:  0.72 (0.24), residues: 486
  sheet: -0.39 (0.49), residues: 132
  loop : -2.15 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 386 
 TYR   0.026   0.002   TYR A 527 
 PHE   0.020   0.002   PHE D  36 
 TRP   0.036   0.002   TRP D  30 
 HIS   0.011   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10123)
  covalent geometry    : angle       0.76338 (13946)
  hydrogen bonds       : bond        0.05850 (  463)
  hydrogen bonds       : angle       4.77318 ( 1289)
  metal coordination   : bond        0.01064 (    4)
  metal coordination   : angle      20.58857 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 191
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8115 (pttp)
REVERT: A  373 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8319 (mp)
REVERT: A  380 GLU cc_start: 0.7338 (tt0) cc_final: 0.7098 (pt0)
REVERT: A  516 MET cc_start: 0.9133 (mmm) cc_final: 0.8715 (mmm)
REVERT: A  536 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8652 (pt0)
REVERT: B  429 MET cc_start: 0.8168 (ptp) cc_final: 0.7528 (ptm)
REVERT: B  432 ARG cc_start: 0.8658 (ttt90) cc_final: 0.7589 (mtt180)
REVERT: B  444 ASP cc_start: 0.8086 (t0) cc_final: 0.7711 (t0)
REVERT: B  479 MET cc_start: 0.6980 (mmp) cc_final: 0.6189 (mmt)
REVERT: B  516 MET cc_start: 0.7500 (tpp) cc_final: 0.6787 (tpp)
REVERT: B  543 THR cc_start: 0.7732 (t) cc_final: 0.7374 (p)
REVERT: C   22 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7713 (mttt)
REVERT: D   10 ASP cc_start: 0.7361 (m-30) cc_final: 0.6992 (m-30)
REVERT: D   29 CYS cc_start: 0.7291 (t) cc_final: 0.6858 (m)
  outliers start: 32
  outliers final: 13
  residues processed: 210
  average time/residue: 0.1327
  time to fit residues: 36.7036
Evaluate side-chains
  163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   66 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 105 optimal weight:    0.3980
   chunk 71 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
A 390 HIS
A 420 ASN
C   3 HIS
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.083400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.068440 restraints weight = 36436.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.070451 restraints weight = 20311.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.071798 restraints weight = 13742.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.072744 restraints weight = 10538.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.073342 restraints weight = 8725.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.6852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.098  10127  Z= 0.357
  Angle     :  1.004  39.706  13958  Z= 0.485
  Chirality :  0.052   0.360   1516
  Planarity :  0.008   0.060   1618
  Dihedral  : 20.258 143.077   1845
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.86 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 16.43 %
    Favored  : 78.94 %
  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 are not related in a simple way.
  whole: -1.11 (0.25), residues: 1072
  helix:  0.43 (0.23), residues: 475
  sheet: -0.30 (0.49), residues: 130
  loop : -2.13 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 544 
 TYR   0.029   0.003   TYR B 232 
 PHE   0.025   0.003   PHE B 407 
 TRP   0.018   0.003   TRP D  30 
 HIS   0.009   0.002   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 (10123)
  covalent geometry    : angle       0.89647 (13946)
  hydrogen bonds       : bond        0.06976 (  463)
  hydrogen bonds       : angle       5.29400 ( 1289)
  metal coordination   : bond        0.02365 (    4)
  metal coordination   : angle      15.44775 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.8985 (tttt) cc_final: 0.8386 (tppp)
REVERT: A  154 ASP cc_start: 0.7685 (t70) cc_final: 0.7280 (p0)
REVERT: A  181 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8390 (mt)
REVERT: A  235 LYS cc_start: 0.9212 (tttt) cc_final: 0.8979 (tttm)
REVERT: A  259 GLN cc_start: 0.7837 (mt0) cc_final: 0.7195 (pt0)
REVERT: A  293 MET cc_start: 0.8238 (mmm) cc_final: 0.7841 (mmm)
REVERT: A  336 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7469 (ttp80)
REVERT: A  394 MET cc_start: 0.7698 (mtp) cc_final: 0.7391 (mtp)
REVERT: A  464 MET cc_start: 0.8973 (mmm) cc_final: 0.8766 (tpt)
REVERT: A  536 GLU cc_start: 0.8783 (pt0) cc_final: 0.8515 (pt0)
REVERT: B  260 VAL cc_start: 0.9014 (t) cc_final: 0.8746 (m)
REVERT: B  377 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8333 (tt)
REVERT: B  429 MET cc_start: 0.8825 (ptp) cc_final: 0.8518 (ptp)
REVERT: B  479 MET cc_start: 0.7733 (mmp) cc_final: 0.7228 (mmt)
REVERT: B  516 MET cc_start: 0.8602 (tpp) cc_final: 0.8391 (tpp)
REVERT: B  536 GLU cc_start: 0.8595 (tt0) cc_final: 0.7955 (mm-30)
REVERT: C   44 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8246 (mmm-85)
REVERT: D    4 LEU cc_start: 0.7952 (mt) cc_final: 0.7695 (mt)
REVERT: D   89 LEU cc_start: 0.9046 (mm) cc_final: 0.8818 (tp)
  outliers start: 42
  outliers final: 22
  residues processed: 190
  average time/residue: 0.1333
  time to fit residues: 33.3433
Evaluate side-chains
  149 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  550 ILE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue   66 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 77 optimal weight:    0.3980
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C   3 HIS
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.085716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.070684 restraints weight = 36414.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.072769 restraints weight = 20104.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.074196 restraints weight = 13493.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.075117 restraints weight = 10252.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.075838 restraints weight = 8497.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.7152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10127  Z= 0.146
  Angle     :  0.719  19.691  13958  Z= 0.357
  Chirality :  0.043   0.149   1516
  Planarity :  0.005   0.041   1618
  Dihedral  : 19.811 140.236   1844
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.29 %
    Favored  : 77.18 %
  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 are not related in a simple way.
  whole: -0.48 (0.25), residues: 1072
  helix:  1.14 (0.24), residues: 473
  sheet:  0.08 (0.50), residues: 122
  loop : -2.01 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 336 
 TYR   0.019   0.001   TYR A 527 
 PHE   0.013   0.001   PHE D  85 
 TRP   0.022   0.002   TRP D  30 
 HIS   0.007   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10123)
  covalent geometry    : angle       0.66702 (13946)
  hydrogen bonds       : bond        0.04663 (  463)
  hydrogen bonds       : angle       4.44283 ( 1289)
  metal coordination   : bond        0.00984 (    4)
  metal coordination   : angle       9.13974 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8949 (mpp) cc_final: 0.8693 (mmt)
REVERT: A  224 LEU cc_start: 0.8823 (tt) cc_final: 0.8353 (tt)
REVERT: A  235 LYS cc_start: 0.9066 (tttt) cc_final: 0.8779 (tttm)
REVERT: A  259 GLN cc_start: 0.7718 (mt0) cc_final: 0.7252 (pt0)
REVERT: A  293 MET cc_start: 0.8095 (mmm) cc_final: 0.7663 (mmm)
REVERT: A  391 PHE cc_start: 0.8613 (t80) cc_final: 0.8389 (t80)
REVERT: A  427 TYR cc_start: 0.8503 (m-10) cc_final: 0.8149 (m-80)
REVERT: A  429 MET cc_start: 0.9033 (ppp) cc_final: 0.8743 (ppp)
REVERT: A  465 MET cc_start: 0.8063 (ppp) cc_final: 0.7842 (ppp)
REVERT: B  429 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8278 (ptp)
REVERT: B  479 MET cc_start: 0.7356 (mmp) cc_final: 0.7102 (mmt)
REVERT: B  516 MET cc_start: 0.8680 (tpp) cc_final: 0.8298 (tpp)
REVERT: B  536 GLU cc_start: 0.8596 (tt0) cc_final: 0.7816 (mm-30)
REVERT: C    2 GLU cc_start: 0.7504 (mp0) cc_final: 0.7215 (mp0)
REVERT: C   44 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8219 (mmm-85)
REVERT: C   83 LYS cc_start: 0.8431 (mttm) cc_final: 0.8213 (mtmm)
REVERT: D    4 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7761 (mt)
  outliers start: 23
  outliers final: 12
  residues processed: 168
  average time/residue: 0.1346
  time to fit residues: 29.7069
Evaluate side-chains
  148 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  429 MET
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue    4 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 108 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 420 ASN
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.082711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.067985 restraints weight = 36404.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.070019 restraints weight = 20060.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.071389 restraints weight = 13464.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.072335 restraints weight = 10223.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.072958 restraints weight = 8440.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.7757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10127  Z= 0.176
  Angle     :  0.712  17.915  13958  Z= 0.350
  Chirality :  0.043   0.157   1516
  Planarity :  0.005   0.043   1618
  Dihedral  : 19.723 139.523   1843
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.53 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 22.49 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1072
  helix:  1.36 (0.24), residues: 473
  sheet:  0.00 (0.50), residues: 123
  loop : -1.91 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 325 
 TYR   0.016   0.002   TYR A 527 
 PHE   0.026   0.002   PHE A 407 
 TRP   0.018   0.002   TRP D  30 
 HIS   0.006   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10123)
  covalent geometry    : angle       0.65897 (13946)
  hydrogen bonds       : bond        0.04778 (  463)
  hydrogen bonds       : angle       4.39641 ( 1289)
  metal coordination   : bond        0.01151 (    4)
  metal coordination   : angle       9.24851 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8969 (mpp) cc_final: 0.8726 (mmt)
REVERT: A  105 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8602 (ttmm)
REVERT: A  235 LYS cc_start: 0.9067 (tttt) cc_final: 0.8776 (tttm)
REVERT: A  259 GLN cc_start: 0.7779 (mt0) cc_final: 0.7239 (pt0)
REVERT: A  293 MET cc_start: 0.8117 (mmm) cc_final: 0.7845 (mmm)
REVERT: A  325 ARG cc_start: 0.7111 (ptp-110) cc_final: 0.6715 (ptp90)
REVERT: A  341 ARG cc_start: 0.7065 (mpt180) cc_final: 0.6787 (tpp-160)
REVERT: A  391 PHE cc_start: 0.8268 (t80) cc_final: 0.7939 (t80)
REVERT: A  394 MET cc_start: 0.7897 (mtm) cc_final: 0.7514 (mtm)
REVERT: A  427 TYR cc_start: 0.8579 (m-10) cc_final: 0.8212 (m-80)
REVERT: A  429 MET cc_start: 0.9049 (ppp) cc_final: 0.8824 (ppp)
REVERT: B  364 MET cc_start: 0.6644 (mtt) cc_final: 0.6384 (tpp)
REVERT: B  387 TYR cc_start: 0.8488 (t80) cc_final: 0.8269 (t80)
REVERT: B  394 MET cc_start: 0.8246 (mmp) cc_final: 0.8003 (mmp)
REVERT: B  479 MET cc_start: 0.7835 (mmp) cc_final: 0.7344 (mmt)
REVERT: B  516 MET cc_start: 0.8752 (tpp) cc_final: 0.8443 (tpp)
REVERT: B  536 GLU cc_start: 0.8642 (tt0) cc_final: 0.7831 (mm-30)
REVERT: C   13 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.7801 (t0)
REVERT: C   44 ARG cc_start: 0.8359 (mtp85) cc_final: 0.7949 (mmm-85)
REVERT: D   67 ASP cc_start: 0.8279 (t0) cc_final: 0.7800 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 162
  average time/residue: 0.1310
  time to fit residues: 27.6334
Evaluate side-chains
  144 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  483 ASN
Chi-restraints excluded: chain A residue  550 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   13 ASN
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain D residue   29 CYS
Chi-restraints excluded: chain D residue   84 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 55 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.083419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.068768 restraints weight = 36596.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.070796 restraints weight = 20012.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.072192 restraints weight = 13370.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073127 restraints weight = 10107.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.073741 restraints weight = 8363.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.7994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10127  Z= 0.135
  Angle     :  0.667  15.576  13958  Z= 0.332
  Chirality :  0.042   0.149   1516
  Planarity :  0.004   0.044   1618
  Dihedral  : 19.654 139.347   1843
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 24.04 %
    Favored  : 73.54 %
  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 are not related in a simple way.
  whole: -0.05 (0.26), residues: 1072
  helix:  1.55 (0.24), residues: 474
  sheet:  0.20 (0.51), residues: 122
  loop : -1.83 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  49 
 TYR   0.017   0.001   TYR A 527 
 PHE   0.020   0.001   PHE A 407 
 TRP   0.019   0.002   TRP D  30 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10123)
  covalent geometry    : angle       0.62718 (13946)
  hydrogen bonds       : bond        0.04187 (  463)
  hydrogen bonds       : angle       4.21905 ( 1289)
  metal coordination   : bond        0.00778 (    4)
  metal coordination   : angle       7.81637 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8596 (ttmm)
REVERT: A  235 LYS cc_start: 0.8958 (tttt) cc_final: 0.8680 (tttm)
REVERT: A  259 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7367 (pt0)
REVERT: A  325 ARG cc_start: 0.6910 (ptp-110) cc_final: 0.6583 (ptp-110)
REVERT: A  391 PHE cc_start: 0.8292 (t80) cc_final: 0.7953 (t80)
REVERT: A  394 MET cc_start: 0.8018 (mtm) cc_final: 0.7693 (mtm)
REVERT: A  427 TYR cc_start: 0.8483 (m-10) cc_final: 0.8052 (m-80)
REVERT: A  429 MET cc_start: 0.9123 (ppp) cc_final: 0.8809 (ppp)
REVERT: A  465 MET cc_start: 0.7880 (ppp) cc_final: 0.7614 (ppp)
REVERT: B  364 MET cc_start: 0.6797 (mtt) cc_final: 0.6584 (tpp)
REVERT: B  394 MET cc_start: 0.8189 (mmp) cc_final: 0.7840 (mmp)
REVERT: B  429 MET cc_start: 0.8686 (ptp) cc_final: 0.8276 (ptp)
REVERT: B  479 MET cc_start: 0.7805 (mmp) cc_final: 0.7291 (mmt)
REVERT: B  506 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8630 (mtmm)
REVERT: B  516 MET cc_start: 0.8779 (tpp) cc_final: 0.8572 (tpp)
REVERT: B  536 GLU cc_start: 0.8593 (tt0) cc_final: 0.8300 (tt0)
REVERT: C   44 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7953 (mmm-85)
  outliers start: 22
  outliers final: 16
  residues processed: 154
  average time/residue: 0.1145
  time to fit residues: 23.5505
Evaluate side-chains
  143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  259 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  483 ASN
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain D residue   65 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3606 r_free = 0.3606 target = 0.082465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.067948 restraints weight = 36486.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.069971 restraints weight = 20032.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.071343 restraints weight = 13446.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.072286 restraints weight = 10266.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.072928 restraints weight = 8464.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.8286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10127  Z= 0.141
  Angle     :  0.673  15.662  13958  Z= 0.334
  Chirality :  0.042   0.147   1516
  Planarity :  0.004   0.045   1618
  Dihedral  : 19.609 139.361   1843
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.16 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 24.15 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.26), residues: 1072
  helix:  1.64 (0.24), residues: 479
  sheet:  0.28 (0.51), residues: 122
  loop : -1.82 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 544 
 TYR   0.016   0.001   TYR A 527 
 PHE   0.017   0.001   PHE A 407 
 TRP   0.021   0.002   TRP A 327 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10123)
  covalent geometry    : angle       0.63412 (13946)
  hydrogen bonds       : bond        0.04126 (  463)
  hydrogen bonds       : angle       4.15501 ( 1289)
  metal coordination   : bond        0.00807 (    4)
  metal coordination   : angle       7.68094 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8379 (mm-30)
REVERT: A  105 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8615 (ttmm)
REVERT: A  235 LYS cc_start: 0.8948 (tttt) cc_final: 0.8648 (tttm)
REVERT: A  259 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7561 (pt0)
REVERT: A  325 ARG cc_start: 0.6902 (ptp-110) cc_final: 0.6557 (ptp-110)
REVERT: A  391 PHE cc_start: 0.8287 (t80) cc_final: 0.7926 (t80)
REVERT: A  394 MET cc_start: 0.8005 (mtm) cc_final: 0.7649 (mtm)
REVERT: A  427 TYR cc_start: 0.8482 (m-10) cc_final: 0.8048 (m-80)
REVERT: A  429 MET cc_start: 0.9147 (ppp) cc_final: 0.8809 (ppp)
REVERT: A  465 MET cc_start: 0.7776 (ppp) cc_final: 0.7558 (ppp)
REVERT: B  259 GLN cc_start: 0.8659 (pt0) cc_final: 0.8034 (pm20)
REVERT: B  394 MET cc_start: 0.8099 (mmp) cc_final: 0.7856 (mmp)
REVERT: B  429 MET cc_start: 0.8619 (ptp) cc_final: 0.8320 (ptp)
REVERT: B  506 LYS cc_start: 0.8961 (ptpt) cc_final: 0.8696 (mtmm)
REVERT: B  516 MET cc_start: 0.8789 (tpp) cc_final: 0.8486 (tpp)
REVERT: B  533 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7211 (ptm-80)
REVERT: B  536 GLU cc_start: 0.8549 (tt0) cc_final: 0.7296 (tt0)
  outliers start: 20
  outliers final: 15
  residues processed: 153
  average time/residue: 0.1291
  time to fit residues: 25.7011
Evaluate side-chains
  145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  259 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  530 SER
Chi-restraints excluded: chain B residue  533 ARG
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   68 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0470
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.083326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.068748 restraints weight = 35814.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.070805 restraints weight = 19485.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.072196 restraints weight = 13013.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.073151 restraints weight = 9876.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.073833 restraints weight = 8138.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.8503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10127  Z= 0.129
  Angle     :  0.665  14.664  13958  Z= 0.330
  Chirality :  0.042   0.147   1516
  Planarity :  0.004   0.044   1618
  Dihedral  : 19.571 138.836   1843
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 24.37 %
    Favored  : 73.10 %
  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 are not related in a simple way.
  whole:  0.18 (0.26), residues: 1072
  helix:  1.76 (0.24), residues: 480
  sheet:  0.59 (0.52), residues: 117
  loop : -1.83 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  90 
 TYR   0.017   0.001   TYR A 527 
 PHE   0.016   0.001   PHE A 407 
 TRP   0.023   0.002   TRP A 327 
 HIS   0.003   0.001   HIS D   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10123)
  covalent geometry    : angle       0.63399 (13946)
  hydrogen bonds       : bond        0.03806 (  463)
  hydrogen bonds       : angle       4.04584 ( 1289)
  metal coordination   : bond        0.00688 (    4)
  metal coordination   : angle       6.82752 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8527 (ttmm)
REVERT: A  235 LYS cc_start: 0.8939 (tttt) cc_final: 0.8627 (tttm)
REVERT: A  236 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (t70)
REVERT: A  259 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7687 (pt0)
REVERT: A  293 MET cc_start: 0.8132 (mmm) cc_final: 0.7883 (mmm)
REVERT: A  325 ARG cc_start: 0.6865 (ptp-110) cc_final: 0.6450 (ptp-110)
REVERT: A  336 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6561 (ttt180)
REVERT: A  394 MET cc_start: 0.7945 (mtm) cc_final: 0.7560 (ttm)
REVERT: A  427 TYR cc_start: 0.8598 (m-10) cc_final: 0.8098 (m-80)
REVERT: A  429 MET cc_start: 0.9149 (ppp) cc_final: 0.8807 (ppp)
REVERT: A  435 THR cc_start: 0.8247 (m) cc_final: 0.8029 (m)
REVERT: A  465 MET cc_start: 0.7673 (ppp) cc_final: 0.7426 (ppp)
REVERT: B  364 MET cc_start: 0.7244 (tpp) cc_final: 0.6541 (mmt)
REVERT: B  394 MET cc_start: 0.8101 (mmp) cc_final: 0.7865 (mmp)
REVERT: B  429 MET cc_start: 0.8570 (ptp) cc_final: 0.8302 (ptp)
REVERT: B  506 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8717 (mtmm)
REVERT: B  516 MET cc_start: 0.8787 (tpp) cc_final: 0.8549 (tpp)
REVERT: D   67 ASP cc_start: 0.8542 (t0) cc_final: 0.7994 (t0)
REVERT: D   83 LYS cc_start: 0.7337 (mtmt) cc_final: 0.7112 (mtmm)
  outliers start: 23
  outliers final: 15
  residues processed: 149
  average time/residue: 0.0977
  time to fit residues: 19.6914
Evaluate side-chains
  146 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  236 ASP
Chi-restraints excluded: chain A residue  259 GLN
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  483 ASN
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  530 SER
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   74 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    0.0570
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.9100

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

Flipped N/Q/H residues before XYZ refinement:
A 131 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.082226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.067882 restraints weight = 36160.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.069886 restraints weight = 19947.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071280 restraints weight = 13420.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.072184 restraints weight = 10151.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.072852 restraints weight = 8393.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.8721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10127  Z= 0.136
  Angle     :  0.687  15.126  13958  Z= 0.339
  Chirality :  0.042   0.166   1516
  Planarity :  0.004   0.045   1618
  Dihedral  : 19.584 138.814   1843
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 25.36 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.26), residues: 1072
  helix:  1.79 (0.24), residues: 479
  sheet:  0.62 (0.52), residues: 117
  loop : -1.79 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  44 
 TYR   0.016   0.001   TYR A 450 
 PHE   0.015   0.001   PHE A 407 
 TRP   0.023   0.002   TRP A 327 
 HIS   0.006   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10123)
  covalent geometry    : angle       0.65347 (13946)
  hydrogen bonds       : bond        0.03912 (  463)
  hydrogen bonds       : angle       4.07234 ( 1289)
  metal coordination   : bond        0.00721 (    4)
  metal coordination   : angle       7.29223 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8916 (mmt) cc_final: 0.8692 (mmm)
REVERT: A  105 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8525 (ttmm)
REVERT: A  235 LYS cc_start: 0.8942 (tttt) cc_final: 0.8629 (tttm)
REVERT: A  259 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7660 (pt0)
REVERT: A  325 ARG cc_start: 0.6817 (ptp-110) cc_final: 0.6384 (ptp-110)
REVERT: A  341 ARG cc_start: 0.6712 (mpt180) cc_final: 0.6421 (tpp-160)
REVERT: A  394 MET cc_start: 0.8003 (mtm) cc_final: 0.7620 (ttm)
REVERT: A  427 TYR cc_start: 0.8498 (m-10) cc_final: 0.8039 (m-80)
REVERT: A  429 MET cc_start: 0.9151 (ppp) cc_final: 0.8912 (ppp)
REVERT: A  435 THR cc_start: 0.8268 (m) cc_final: 0.8051 (m)
REVERT: B  394 MET cc_start: 0.8198 (mmp) cc_final: 0.7953 (mmp)
REVERT: B  429 MET cc_start: 0.8557 (ptp) cc_final: 0.8327 (ptp)
REVERT: B  506 LYS cc_start: 0.9022 (ptpt) cc_final: 0.8731 (mtmm)
REVERT: B  516 MET cc_start: 0.8846 (tpp) cc_final: 0.8563 (tpp)
REVERT: B  536 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7932 (mm-30)
REVERT: D   67 ASP cc_start: 0.8623 (t0) cc_final: 0.8417 (t0)
REVERT: D   83 LYS cc_start: 0.7387 (mtmt) cc_final: 0.7179 (mtmm)
  outliers start: 17
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1155
  time to fit residues: 22.8404
Evaluate side-chains
  147 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  259 GLN
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  530 SER
Chi-restraints excluded: chain B residue  536 GLU
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   68 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.0670
   chunk 108 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0570
   chunk 95 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    0.9838

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

Flipped N/Q/H residues before XYZ refinement:
D  62 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.081713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.067345 restraints weight = 36434.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.069363 restraints weight = 20223.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.070738 restraints weight = 13634.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.071679 restraints weight = 10385.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.072296 restraints weight = 8575.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.8960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10127  Z= 0.141
  Angle     :  0.703  15.463  13958  Z= 0.345
  Chirality :  0.042   0.157   1516
  Planarity :  0.004   0.061   1618
  Dihedral  : 19.558 138.752   1843
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 25.80 %
    Favored  : 72.44 %
  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 are not related in a simple way.
  whole:  0.29 (0.26), residues: 1072
  helix:  1.84 (0.24), residues: 479
  sheet:  0.74 (0.53), residues: 115
  loop : -1.77 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  90 
 TYR   0.016   0.001   TYR A 527 
 PHE   0.020   0.001   PHE A 292 
 TRP   0.026   0.002   TRP A 327 
 HIS   0.009   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10123)
  covalent geometry    : angle       0.66873 (13946)
  hydrogen bonds       : bond        0.03915 (  463)
  hydrogen bonds       : angle       4.07454 ( 1289)
  metal coordination   : bond        0.00742 (    4)
  metal coordination   : angle       7.47759 (   12)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8931 (mmt) cc_final: 0.8690 (mmm)
REVERT: A  105 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8515 (ttmm)
REVERT: A  235 LYS cc_start: 0.8930 (tttt) cc_final: 0.8665 (tttm)
REVERT: A  259 GLN cc_start: 0.8143 (mt0) cc_final: 0.7714 (pt0)
REVERT: A  325 ARG cc_start: 0.6838 (ptp-110) cc_final: 0.6395 (ptp-110)
REVERT: A  341 ARG cc_start: 0.6734 (mpt180) cc_final: 0.6453 (tpp-160)
REVERT: A  391 PHE cc_start: 0.8309 (t80) cc_final: 0.7961 (t80)
REVERT: A  394 MET cc_start: 0.8074 (mtm) cc_final: 0.7650 (ttm)
REVERT: A  427 TYR cc_start: 0.8497 (m-10) cc_final: 0.8039 (m-80)
REVERT: A  429 MET cc_start: 0.9149 (ppp) cc_final: 0.8911 (ppp)
REVERT: A  435 THR cc_start: 0.8298 (m) cc_final: 0.8084 (m)
REVERT: A  465 MET cc_start: 0.7949 (ppp) cc_final: 0.7692 (ppp)
REVERT: B  222 LEU cc_start: 0.8437 (mt) cc_final: 0.8221 (mp)
REVERT: B  259 GLN cc_start: 0.9134 (pt0) cc_final: 0.8889 (pt0)
REVERT: B  364 MET cc_start: 0.7200 (mmm) cc_final: 0.6538 (mmt)
REVERT: B  394 MET cc_start: 0.8290 (mmp) cc_final: 0.8040 (mmp)
REVERT: B  506 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8691 (mtmm)
REVERT: B  516 MET cc_start: 0.8851 (tpp) cc_final: 0.8557 (tpp)
REVERT: B  536 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7976 (mm-30)
REVERT: D   67 ASP cc_start: 0.8609 (t0) cc_final: 0.8314 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1017
  time to fit residues: 19.6119
Evaluate side-chains
  145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  530 SER
Chi-restraints excluded: chain B residue  536 GLU
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   68 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0270
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0970
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
B 274 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.082319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068109 restraints weight = 36949.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.070111 restraints weight = 20637.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071499 restraints weight = 13966.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072432 restraints weight = 10622.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.073030 restraints weight = 8772.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.9099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10127  Z= 0.129
  Angle     :  0.689  14.607  13958  Z= 0.339
  Chirality :  0.042   0.152   1516
  Planarity :  0.004   0.048   1618
  Dihedral  : 19.485 138.547   1843
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 25.69 %
    Favored  : 72.33 %
  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 are not related in a simple way.
  whole:  0.40 (0.26), residues: 1072
  helix:  1.96 (0.25), residues: 474
  sheet:  0.78 (0.53), residues: 115
  loop : -1.72 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 396 
 TYR   0.016   0.001   TYR A 527 
 PHE   0.015   0.001   PHE A 407 
 TRP   0.025   0.002   TRP A 327 
 HIS   0.007   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10123)
  covalent geometry    : angle       0.66030 (13946)
  hydrogen bonds       : bond        0.03670 (  463)
  hydrogen bonds       : angle       4.00455 ( 1289)
  metal coordination   : bond        0.00617 (    4)
  metal coordination   : angle       6.71954 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1657.29 seconds
wall clock time: 29 minutes 13.29 seconds (1753.29 seconds total)