Starting phenix.real_space_refine
on Sun Jul 27 22:42:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mid_23847/07_2025/7mid_23847.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mid_23847/07_2025/7mid_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2025/7mid_23847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2025/7mid_23847.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2025/7mid_23847.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2025/7mid_23847.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.86, per 1000 atoms: 0.60
  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: 2.54
  Conformation dependent library (CDL) restraints added in 982.6 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: 3.35
  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: 3.38

  Time building geometry restraints manager: 2.97 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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     28.700
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.660
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (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
 TRP   0.014   0.002   TRP D  30 
 HIS   0.011   0.002   HIS B 522 
 PHE   0.022   0.002   PHE B 425 
 TYR   0.019   0.002   TYR B 545 
 ARG   0.133   0.002   ARG A 146 

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

*********************** 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  : 1.414 
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: symmetry clash
REVERT: A  233 VAL cc_start: 0.8896 (t) cc_final: 0.8614 (t)
REVERT: A  335 CYS cc_start: 0.4388 (m) cc_final: 0.4112 (m)
REVERT: A  516 MET cc_start: 0.8354 (mmm) cc_final: 0.8127 (mmm)
REVERT: B  432 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7453 (mtt180)
REVERT: B  479 MET cc_start: 0.7090 (mmp) cc_final: 0.6644 (mmt)
REVERT: B  509 ILE cc_start: 0.8087 (mt) cc_final: 0.7715 (mm)
  outliers start: 52
  outliers final: 9
  residues processed: 339
  average time/residue: 0.3550
  time to fit residues: 151.9151
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  : 0.967 
-------------------------------------------------------------------------------
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 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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  25 HIS
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 = 0.3957 r_free = 0.3957 target = 0.105004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.089845 restraints weight = 38123.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.092224 restraints weight = 21243.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.093866 restraints weight = 14139.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  10127  Z= 0.185
  Angle     :  0.978  44.123  13958  Z= 0.416
  Chirality :  0.047   0.162   1516
  Planarity :  0.006   0.067   1618
  Dihedral  : 20.072 140.250   1862
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.16 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.44 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.26), residues: 1072
  helix:  0.84 (0.24), residues: 480
  sheet: -0.10 (0.50), residues: 124
  loop : -2.22 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP D  30 
 HIS   0.011   0.001   HIS B 390 
 PHE   0.021   0.002   PHE D  36 
 TYR   0.026   0.002   TYR A 527 
 ARG   0.008   0.001   ARG A 344 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05481 (  463)
  hydrogen bonds       : angle       4.72695 ( 1289)
  metal coordination   : bond        0.00993 (    4)
  metal coordination   : angle      20.01980 (   12)
  covalent geometry    : bond        0.00420 (10123)
  covalent geometry    : angle       0.78301 (13946)

*********************** 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
  225 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 0.968 
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: A   34 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8403 (mm-30)
REVERT: A  105 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8803 (mmmm)
REVERT: A  230 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8104 (pttp)
REVERT: A  373 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8294 (mp)
REVERT: A  380 GLU cc_start: 0.7419 (tt0) cc_final: 0.7128 (pt0)
REVERT: A  516 MET cc_start: 0.9156 (mmm) cc_final: 0.8694 (mmm)
REVERT: A  536 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8697 (pt0)
REVERT: B  225 TYR cc_start: 0.5589 (m-10) cc_final: 0.5289 (m-10)
REVERT: B  236 ASP cc_start: 0.7228 (t0) cc_final: 0.7011 (m-30)
REVERT: B  364 MET cc_start: 0.4532 (mtm) cc_final: 0.4195 (mtt)
REVERT: B  429 MET cc_start: 0.8305 (ptp) cc_final: 0.7693 (ptm)
REVERT: B  432 ARG cc_start: 0.8685 (ttt90) cc_final: 0.7611 (mtt180)
REVERT: B  444 ASP cc_start: 0.8083 (t0) cc_final: 0.7730 (t0)
REVERT: B  464 MET cc_start: 0.8445 (tpp) cc_final: 0.8225 (tpp)
REVERT: B  479 MET cc_start: 0.7038 (mmp) cc_final: 0.6240 (mmt)
REVERT: B  516 MET cc_start: 0.7508 (tpp) cc_final: 0.6961 (tpp)
REVERT: B  543 THR cc_start: 0.7768 (t) cc_final: 0.7403 (p)
REVERT: D   10 ASP cc_start: 0.7380 (m-30) cc_final: 0.7014 (m-30)
REVERT: D   29 CYS cc_start: 0.7411 (t) cc_final: 0.6961 (m)
REVERT: D   40 LEU cc_start: 0.7958 (mp) cc_final: 0.6958 (mp)
REVERT: D   67 ASP cc_start: 0.7744 (t0) cc_final: 0.7428 (m-30)
  outliers start: 32
  outliers final: 12
  residues processed: 213
  average time/residue: 0.2615
  time to fit residues: 74.4156
Evaluate side-chains
  170 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
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  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 45 optimal weight:    0.0370
   chunk 80 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0170
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.8102

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.090541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075318 restraints weight = 36609.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.077482 restraints weight = 20333.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.078943 restraints weight = 13620.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10127  Z= 0.217
  Angle     :  0.819  28.789  13958  Z= 0.401
  Chirality :  0.047   0.253   1516
  Planarity :  0.007   0.092   1618
  Dihedral  : 19.920 141.867   1845
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.55 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1072
  helix:  1.01 (0.24), residues: 478
  sheet: -0.13 (0.50), residues: 124
  loop : -2.09 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP D  30 
 HIS   0.008   0.002   HIS C   3 
 PHE   0.025   0.002   PHE B 407 
 TYR   0.026   0.002   TYR B 232 
 ARG   0.015   0.001   ARG B 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05518 (  463)
  hydrogen bonds       : angle       4.67271 ( 1289)
  metal coordination   : bond        0.01225 (    4)
  metal coordination   : angle      11.42488 (   12)
  covalent geometry    : bond        0.00479 (10123)
  covalent geometry    : angle       0.74782 (13946)

*********************** 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
  200 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 0.986 
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: A  154 ASP cc_start: 0.7608 (t70) cc_final: 0.7091 (p0)
REVERT: A  230 LYS cc_start: 0.8602 (pttp) cc_final: 0.8313 (pttp)
REVERT: A  259 GLN cc_start: 0.8052 (mt0) cc_final: 0.7396 (pt0)
REVERT: A  280 GLU cc_start: 0.9267 (pm20) cc_final: 0.8912 (mp0)
REVERT: A  293 MET cc_start: 0.8117 (mmm) cc_final: 0.7730 (mmm)
REVERT: A  427 TYR cc_start: 0.8557 (m-10) cc_final: 0.8206 (m-80)
REVERT: A  429 MET cc_start: 0.9130 (ppp) cc_final: 0.8844 (ppp)
REVERT: A  536 GLU cc_start: 0.8883 (pt0) cc_final: 0.8680 (pt0)
REVERT: B  259 GLN cc_start: 0.9075 (pt0) cc_final: 0.8830 (pt0)
REVERT: B  429 MET cc_start: 0.8598 (ptp) cc_final: 0.8266 (ptp)
REVERT: B  479 MET cc_start: 0.7685 (mmp) cc_final: 0.7393 (mmt)
REVERT: B  516 MET cc_start: 0.8433 (tpp) cc_final: 0.8142 (tpp)
REVERT: C   20 LEU cc_start: 0.9280 (tp) cc_final: 0.9036 (tp)
REVERT: C   23 THR cc_start: 0.9127 (m) cc_final: 0.8787 (p)
REVERT: C   44 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8200 (mmm-85)
REVERT: D   29 CYS cc_start: 0.7848 (t) cc_final: 0.7638 (t)
REVERT: D   44 ARG cc_start: 0.7208 (mmm-85) cc_final: 0.5858 (tpt170)
REVERT: D   45 ILE cc_start: 0.8396 (pt) cc_final: 0.7925 (pt)
REVERT: D   67 ASP cc_start: 0.8092 (t0) cc_final: 0.7762 (t0)
REVERT: D   86 ASP cc_start: 0.8641 (t0) cc_final: 0.8414 (t0)
  outliers start: 33
  outliers final: 19
  residues processed: 192
  average time/residue: 0.2606
  time to fit residues: 66.8403
Evaluate side-chains
  149 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
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  166 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  377 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  550 ILE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  365 ARG
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    6 ILE
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 14 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   overall best weight:    1.1704

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.089075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.074113 restraints weight = 36258.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.076245 restraints weight = 20010.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.077742 restraints weight = 13376.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.6500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10127  Z= 0.151
  Angle     :  0.700  16.268  13958  Z= 0.346
  Chirality :  0.043   0.146   1516
  Planarity :  0.005   0.042   1618
  Dihedral  : 19.567 139.692   1841
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.30 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.26), residues: 1072
  helix:  1.50 (0.24), residues: 471
  sheet:  0.18 (0.51), residues: 124
  loop : -2.00 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  30 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.021   0.001   PHE A 407 
 TYR   0.019   0.002   TYR A 527 
 ARG   0.005   0.001   ARG A 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04345 (  463)
  hydrogen bonds       : angle       4.25880 ( 1289)
  metal coordination   : bond        0.01053 (    4)
  metal coordination   : angle       8.60395 (   12)
  covalent geometry    : bond        0.00338 (10123)
  covalent geometry    : angle       0.65280 (13946)

*********************** 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
  172 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASP cc_start: 0.7611 (t70) cc_final: 0.7196 (p0)
REVERT: A  230 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8270 (pttp)
REVERT: A  259 GLN cc_start: 0.7847 (mt0) cc_final: 0.7301 (pt0)
REVERT: A  280 GLU cc_start: 0.9212 (pm20) cc_final: 0.8871 (mp0)
REVERT: A  293 MET cc_start: 0.8177 (mmm) cc_final: 0.7859 (mmm)
REVERT: A  325 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6401 (mtm-85)
REVERT: A  380 GLU cc_start: 0.7722 (tt0) cc_final: 0.7314 (pt0)
REVERT: A  427 TYR cc_start: 0.8567 (m-10) cc_final: 0.8148 (m-80)
REVERT: A  429 MET cc_start: 0.9042 (ppp) cc_final: 0.8781 (ppp)
REVERT: B  429 MET cc_start: 0.8526 (ptp) cc_final: 0.8311 (ptp)
REVERT: B  479 MET cc_start: 0.7672 (mmp) cc_final: 0.7190 (mmt)
REVERT: B  513 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8694 (tp30)
REVERT: B  516 MET cc_start: 0.8497 (tpp) cc_final: 0.8115 (tpp)
REVERT: C   23 THR cc_start: 0.9195 (m) cc_final: 0.8883 (p)
REVERT: C   44 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7900 (mmm-85)
REVERT: D   29 CYS cc_start: 0.7470 (t) cc_final: 0.7238 (t)
REVERT: D   44 ARG cc_start: 0.6976 (mmm-85) cc_final: 0.6560 (tpt-90)
REVERT: D   67 ASP cc_start: 0.8187 (t0) cc_final: 0.7872 (t0)
  outliers start: 24
  outliers final: 14
  residues processed: 166
  average time/residue: 0.2761
  time to fit residues: 61.1729
Evaluate side-chains
  144 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  365 ARG
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   66 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3560 r_free = 0.3560 target = 0.079634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.064932 restraints weight = 36795.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.066927 restraints weight = 20343.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.068265 restraints weight = 13753.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.7835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  10127  Z= 0.275
  Angle     :  0.807  19.574  13958  Z= 0.397
  Chirality :  0.047   0.207   1516
  Planarity :  0.006   0.077   1618
  Dihedral  : 19.761 140.541   1840
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.28 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.25), residues: 1072
  helix:  1.31 (0.24), residues: 471
  sheet:  0.35 (0.50), residues: 121
  loop : -1.97 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 285 
 HIS   0.006   0.001   HIS C  25 
 PHE   0.022   0.002   PHE A 407 
 TYR   0.014   0.002   TYR A 527 
 ARG   0.016   0.001   ARG D  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05698 (  463)
  hydrogen bonds       : angle       4.61309 ( 1289)
  metal coordination   : bond        0.01361 (    4)
  metal coordination   : angle      11.03014 (   12)
  covalent geometry    : bond        0.00595 (10123)
  covalent geometry    : angle       0.73971 (13946)

*********************** 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
  150 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8475 (pttt)
REVERT: A  259 GLN cc_start: 0.7702 (mt0) cc_final: 0.7125 (pt0)
REVERT: A  293 MET cc_start: 0.8151 (mmm) cc_final: 0.7873 (mmm)
REVERT: A  429 MET cc_start: 0.9126 (ppp) cc_final: 0.8847 (tmm)
REVERT: A  465 MET cc_start: 0.7945 (ppp) cc_final: 0.7705 (ppp)
REVERT: B  342 ASN cc_start: 0.8351 (m-40) cc_final: 0.7916 (m-40)
REVERT: B  387 TYR cc_start: 0.8545 (t80) cc_final: 0.8343 (t80)
REVERT: B  479 MET cc_start: 0.8037 (mmp) cc_final: 0.7399 (mmt)
REVERT: B  483 ASN cc_start: 0.6608 (m-40) cc_final: 0.6394 (m-40)
REVERT: B  516 MET cc_start: 0.8863 (tpp) cc_final: 0.8572 (tpp)
REVERT: C   13 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.7922 (t0)
REVERT: C   23 THR cc_start: 0.9274 (m) cc_final: 0.8942 (p)
REVERT: C   44 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8127 (mmm-85)
REVERT: D   29 CYS cc_start: 0.8066 (t) cc_final: 0.7833 (t)
REVERT: D   44 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.6527 (ttt-90)
REVERT: D   67 ASP cc_start: 0.8345 (t0) cc_final: 0.8037 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 142
  average time/residue: 0.2761
  time to fit residues: 51.8678
Evaluate side-chains
  122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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  177 MET
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 SER
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 B residue  366 HIS
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   13 ASN
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   66 LEU
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 7 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 390 HIS ** 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 = 0.3593 r_free = 0.3593 target = 0.081244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.066541 restraints weight = 36010.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.068596 restraints weight = 19574.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.069982 restraints weight = 13084.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.8145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10127  Z= 0.149
  Angle     :  0.691  18.315  13958  Z= 0.342
  Chirality :  0.043   0.142   1516
  Planarity :  0.004   0.047   1618
  Dihedral  : 19.651 139.922   1840
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.49 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1072
  helix:  1.57 (0.24), residues: 472
  sheet:  0.26 (0.51), residues: 122
  loop : -1.91 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  30 
 HIS   0.003   0.001   HIS D   3 
 PHE   0.020   0.001   PHE A 407 
 TYR   0.017   0.001   TYR A 527 
 ARG   0.005   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04484 (  463)
  hydrogen bonds       : angle       4.23000 ( 1289)
  metal coordination   : bond        0.00907 (    4)
  metal coordination   : angle       8.58805 (   12)
  covalent geometry    : bond        0.00334 (10123)
  covalent geometry    : angle       0.64361 (13946)

*********************** 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
  152 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8397 (pttt)
REVERT: A  259 GLN cc_start: 0.7674 (mt0) cc_final: 0.7228 (pt0)
REVERT: A  293 MET cc_start: 0.8196 (mmm) cc_final: 0.7900 (mmm)
REVERT: A  325 ARG cc_start: 0.7329 (mtt180) cc_final: 0.6700 (mtm-85)
REVERT: A  427 TYR cc_start: 0.8582 (m-10) cc_final: 0.8257 (m-80)
REVERT: A  429 MET cc_start: 0.9124 (ppp) cc_final: 0.8850 (ppp)
REVERT: A  465 MET cc_start: 0.7905 (ppp) cc_final: 0.7554 (ppp)
REVERT: A  533 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8558 (mmm-85)
REVERT: B  244 GLU cc_start: 0.7497 (tp30) cc_final: 0.7112 (tp30)
REVERT: B  403 MET cc_start: 0.5958 (mpp) cc_final: 0.5623 (mpp)
REVERT: B  429 MET cc_start: 0.8695 (ptp) cc_final: 0.8264 (ptp)
REVERT: B  516 MET cc_start: 0.8847 (tpp) cc_final: 0.8557 (tpp)
REVERT: B  536 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: D   29 CYS cc_start: 0.7448 (t) cc_final: 0.7201 (t)
REVERT: D   67 ASP cc_start: 0.8388 (t0) cc_final: 0.8038 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 147
  average time/residue: 0.2508
  time to fit residues: 49.6399
Evaluate side-chains
  137 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  230 LYS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  357 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  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  366 HIS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 111 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.080382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.065852 restraints weight = 37041.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.067856 restraints weight = 20405.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.069222 restraints weight = 13737.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.8553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10127  Z= 0.161
  Angle     :  0.687  17.443  13958  Z= 0.337
  Chirality :  0.043   0.142   1516
  Planarity :  0.004   0.048   1618
  Dihedral  : 19.603 139.785   1840
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.82 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.26), residues: 1072
  helix:  1.61 (0.24), residues: 478
  sheet:  0.41 (0.51), residues: 123
  loop : -1.92 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 327 
 HIS   0.005   0.001   HIS B 390 
 PHE   0.017   0.001   PHE A 407 
 TYR   0.014   0.001   TYR A 527 
 ARG   0.008   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04446 (  463)
  hydrogen bonds       : angle       4.18257 ( 1289)
  metal coordination   : bond        0.00979 (    4)
  metal coordination   : angle       8.56745 (   12)
  covalent geometry    : bond        0.00367 (10123)
  covalent geometry    : angle       0.63925 (13946)

*********************** 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
  153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.960 
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: A  230 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8266 (pttp)
REVERT: A  259 GLN cc_start: 0.7743 (mt0) cc_final: 0.7277 (pt0)
REVERT: A  325 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7071 (mtm-85)
REVERT: A  394 MET cc_start: 0.8087 (mtm) cc_final: 0.7637 (mtt)
REVERT: A  427 TYR cc_start: 0.8553 (m-10) cc_final: 0.8187 (m-80)
REVERT: A  429 MET cc_start: 0.9147 (ppp) cc_final: 0.8856 (tmm)
REVERT: A  435 THR cc_start: 0.8376 (m) cc_final: 0.8162 (m)
REVERT: A  465 MET cc_start: 0.7800 (ppp) cc_final: 0.7309 (ppp)
REVERT: B  394 MET cc_start: 0.8301 (mmp) cc_final: 0.7959 (mmp)
REVERT: B  403 MET cc_start: 0.6101 (mpp) cc_final: 0.5783 (mpp)
REVERT: B  429 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8542 (ptp)
REVERT: B  492 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8351 (m)
REVERT: B  506 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8479 (mtmm)
REVERT: B  516 MET cc_start: 0.8884 (tpp) cc_final: 0.8589 (tpp)
REVERT: C   13 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.7842 (t0)
REVERT: D   29 CYS cc_start: 0.7455 (t) cc_final: 0.7215 (t)
REVERT: D   44 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.6896 (mmm-85)
REVERT: D   67 ASP cc_start: 0.8493 (t0) cc_final: 0.8158 (t0)
  outliers start: 27
  outliers final: 19
  residues processed: 148
  average time/residue: 0.2578
  time to fit residues: 51.3285
Evaluate side-chains
  141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  419 VAL
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  550 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  429 MET
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   13 ASN
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 14 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:    0.3980
   chunk 105 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 274 HIS
** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.081075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.066577 restraints weight = 36886.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.068592 restraints weight = 20346.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.069947 restraints weight = 13666.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.8732

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= 0.134
  Angle     :  0.664  16.154  13958  Z= 0.328
  Chirality :  0.042   0.143   1516
  Planarity :  0.004   0.048   1618
  Dihedral  : 19.553 139.276   1840
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.48 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.26), residues: 1072
  helix:  1.74 (0.24), residues: 477
  sheet:  0.59 (0.52), residues: 117
  loop : -1.97 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 327 
 HIS   0.004   0.001   HIS B 390 
 PHE   0.017   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A 527 
 ARG   0.005   0.000   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  463)
  hydrogen bonds       : angle       4.05812 ( 1289)
  metal coordination   : bond        0.00812 (    4)
  metal coordination   : angle       7.58114 (   12)
  covalent geometry    : bond        0.00298 (10123)
  covalent geometry    : angle       0.62589 (13946)

*********************** 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
  159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 1.029 
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: A  230 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8216 (pttp)
REVERT: A  259 GLN cc_start: 0.7696 (mt0) cc_final: 0.7269 (pt0)
REVERT: A  427 TYR cc_start: 0.8555 (m-10) cc_final: 0.8173 (m-80)
REVERT: A  429 MET cc_start: 0.9140 (ppp) cc_final: 0.8863 (tmm)
REVERT: A  435 THR cc_start: 0.8348 (m) cc_final: 0.8138 (m)
REVERT: A  465 MET cc_start: 0.7861 (ppp) cc_final: 0.7516 (ppp)
REVERT: B  394 MET cc_start: 0.8261 (mmp) cc_final: 0.7935 (mmp)
REVERT: B  429 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8279 (ptp)
REVERT: B  479 MET cc_start: 0.7956 (mmp) cc_final: 0.7523 (mtt)
REVERT: B  492 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8329 (m)
REVERT: B  502 ASP cc_start: 0.8234 (m-30) cc_final: 0.7946 (p0)
REVERT: B  506 LYS cc_start: 0.8838 (ptpt) cc_final: 0.8472 (mtmm)
REVERT: B  516 MET cc_start: 0.8854 (tpp) cc_final: 0.8613 (tpp)
REVERT: C   13 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.7770 (t0)
REVERT: D   29 CYS cc_start: 0.7381 (t) cc_final: 0.7147 (t)
REVERT: D   67 ASP cc_start: 0.8443 (t0) cc_final: 0.8109 (t0)
  outliers start: 24
  outliers final: 14
  residues processed: 153
  average time/residue: 0.2780
  time to fit residues: 56.4283
Evaluate side-chains
  140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  429 MET
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  509 ILE
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   78 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.080132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.065875 restraints weight = 36793.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.067842 restraints weight = 20400.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.069224 restraints weight = 13784.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.8970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10127  Z= 0.154
  Angle     :  0.709  16.356  13958  Z= 0.350
  Chirality :  0.042   0.140   1516
  Planarity :  0.004   0.048   1618
  Dihedral  : 19.532 139.236   1840
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 24.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1072
  helix:  1.85 (0.25), residues: 472
  sheet:  0.60 (0.52), residues: 117
  loop : -1.93 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 327 
 HIS   0.006   0.001   HIS D   3 
 PHE   0.016   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A 288 
 ARG   0.008   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  463)
  hydrogen bonds       : angle       4.06648 ( 1289)
  metal coordination   : bond        0.01005 (    4)
  metal coordination   : angle       7.95792 (   12)
  covalent geometry    : bond        0.00349 (10123)
  covalent geometry    : angle       0.66978 (13946)

*********************** 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
  147 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8215 (pttp)
REVERT: A  259 GLN cc_start: 0.7753 (mt0) cc_final: 0.7309 (pt0)
REVERT: A  325 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6723 (mtm-85)
REVERT: A  427 TYR cc_start: 0.8557 (m-10) cc_final: 0.8203 (m-80)
REVERT: A  429 MET cc_start: 0.9137 (ppp) cc_final: 0.8852 (tmm)
REVERT: A  435 THR cc_start: 0.8390 (m) cc_final: 0.8178 (m)
REVERT: A  465 MET cc_start: 0.7869 (ppp) cc_final: 0.7538 (ppp)
REVERT: B  394 MET cc_start: 0.8424 (mmp) cc_final: 0.8113 (mmp)
REVERT: B  479 MET cc_start: 0.8097 (mmp) cc_final: 0.7720 (mtp)
REVERT: B  492 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (m)
REVERT: B  502 ASP cc_start: 0.8285 (m-30) cc_final: 0.7950 (p0)
REVERT: B  506 LYS cc_start: 0.8883 (ptpt) cc_final: 0.8516 (mtmm)
REVERT: B  516 MET cc_start: 0.8859 (tpp) cc_final: 0.8606 (tpp)
REVERT: C   13 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7810 (t0)
REVERT: D   29 CYS cc_start: 0.7353 (t) cc_final: 0.7142 (t)
REVERT: D   67 ASP cc_start: 0.8497 (t0) cc_final: 0.8132 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.3625
  time to fit residues: 68.9580
Evaluate side-chains
  140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
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  190 CYS
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  550 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  509 ILE
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   10 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0050
   chunk 76 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.080399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.066157 restraints weight = 37854.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.068215 restraints weight = 20706.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.069641 restraints weight = 13876.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.9134

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= 0.140
  Angle     :  0.694  15.898  13958  Z= 0.340
  Chirality :  0.042   0.150   1516
  Planarity :  0.004   0.048   1618
  Dihedral  : 19.456 138.699   1840
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 24.70 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1072
  helix:  1.90 (0.25), residues: 472
  sheet:  0.69 (0.51), residues: 117
  loop : -1.93 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 327 
 HIS   0.004   0.001   HIS B 390 
 PHE   0.017   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A 527 
 ARG   0.006   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03969 (  463)
  hydrogen bonds       : angle       4.02606 ( 1289)
  metal coordination   : bond        0.00779 (    4)
  metal coordination   : angle       7.50285 (   12)
  covalent geometry    : bond        0.00312 (10123)
  covalent geometry    : angle       0.65823 (13946)

********************** 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
  153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.982 
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: 0.8666 (OUTLIER) cc_final: 0.8308 (pttt)
REVERT: A  259 GLN cc_start: 0.7756 (mt0) cc_final: 0.7324 (pt0)
REVERT: A  325 ARG cc_start: 0.7404 (mtt180) cc_final: 0.6712 (mtm-85)
REVERT: A  427 TYR cc_start: 0.8534 (m-10) cc_final: 0.8130 (m-80)
REVERT: A  429 MET cc_start: 0.9163 (ppp) cc_final: 0.8880 (tmm)
REVERT: A  435 THR cc_start: 0.8326 (m) cc_final: 0.8119 (m)
REVERT: A  465 MET cc_start: 0.7834 (ppp) cc_final: 0.7489 (ppp)
REVERT: B  353 PRO cc_start: 0.6060 (Cg_exo) cc_final: 0.5720 (Cg_endo)
REVERT: B  394 MET cc_start: 0.8449 (mmp) cc_final: 0.7870 (mpp)
REVERT: B  502 ASP cc_start: 0.8155 (m-30) cc_final: 0.7950 (p0)
REVERT: B  506 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8493 (mtmm)
REVERT: B  516 MET cc_start: 0.8879 (tpp) cc_final: 0.8598 (tpp)
REVERT: C   13 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7757 (t0)
REVERT: D   29 CYS cc_start: 0.7371 (t) cc_final: 0.7151 (t)
REVERT: D   44 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7092 (mmm-85)
REVERT: D   67 ASP cc_start: 0.8446 (t0) cc_final: 0.8123 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 146
  average time/residue: 0.2759
  time to fit residues: 53.5627
Evaluate side-chains
  141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  550 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain C residue   13 ASN
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 33 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 131 HIS
** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3569 r_free = 0.3569 target = 0.079705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.065410 restraints weight = 37078.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.067418 restraints weight = 20539.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.068774 restraints weight = 13879.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.9364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10127  Z= 0.146
  Angle     :  0.695  16.234  13958  Z= 0.341
  Chirality :  0.042   0.144   1516
  Planarity :  0.004   0.049   1618
  Dihedral  : 19.395 139.297   1840
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 24.70 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 1072
  helix:  1.98 (0.25), residues: 472
  sheet:  0.72 (0.52), residues: 116
  loop : -1.89 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  30 
 HIS   0.010   0.001   HIS A 131 
 PHE   0.017   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A 288 
 ARG   0.008   0.001   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  463)
  hydrogen bonds       : angle       4.01485 ( 1289)
  metal coordination   : bond        0.00846 (    4)
  metal coordination   : angle       7.84752 (   12)
  covalent geometry    : bond        0.00333 (10123)
  covalent geometry    : angle       0.65659 (13946)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3726.45 seconds
wall clock time: 66 minutes 43.42 seconds (4003.42 seconds total)