Starting phenix.real_space_refine
on Sat May  2 21:37:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u7i_63937/05_2026/9u7i_63937.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u7i_63937/05_2026/9u7i_63937.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u7i_63937/05_2026/9u7i_63937.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u7i_63937/05_2026/9u7i_63937.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u7i_63937/05_2026/9u7i_63937.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u7i_63937/05_2026/9u7i_63937.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       4      5.49       5
     S      50      5.16       5
     C    5488      2.51       5
     N    1518      2.21       5
     O    1550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8612
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "a"
      Number of atoms: 4277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 522, 4277
          Classifications: {'peptide': 522}
          Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 486}
    Chain: "A"
      Number of atoms: 4261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4261
          Classifications: {'peptide': 520}
          Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 484}
    Chain: "a"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {' MN': 1, 'GDU': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {' MN': 1, 'GDU': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.99, per 1000 atoms: 0.23
  Number of scatterers: 8612
  At special positions: 0
  Unit cell: (159.248, 87.156, 126.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      50     16.00
     P       4     15.00
     O    1550      8.00
     N    1518      7.00
     C    5488      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS a 228 " - pdb=" SG  CYS a 283 " distance=2.31

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 314.3 milliseconds
  

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2016

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      34.4% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'a' and resid 66 through 75
      removed outlier: 3.822A  pdb=" N   GLY a  72 " --> pdb=" O   PRO a  68 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA a  73 " --> pdb=" O   THR a  69 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 80 through 82
      No H-bonds generated for 'chain 'a' and resid 80 through 82'
    Processing helix  chain 'a' and resid 96 through 107
      removed outlier: 3.668A  pdb=" N   ARG a 102 " --> pdb=" O   SER a  98 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA a 107 " --> pdb=" O   GLU a 103 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 108 through 112
      removed outlier: 3.809A  pdb=" N   TYR a 112 " --> pdb=" O   LYS a 109 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 136 through 156
      removed outlier: 3.518A  pdb=" N   TYR a 140 " --> pdb=" O   SER a 136 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU a 141 " --> pdb=" O   ASP a 137 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   HIS a 142 " --> pdb=" O   SER a 138 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 175 through 182
    Processing helix  chain 'a' and resid 216 through 222
      removed outlier: 3.753A  pdb=" N   ILE a 220 " --> pdb=" O   ALA a 216 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 244 through 249
      removed outlier: 4.082A  pdb=" N   ARG a 248 " --> pdb=" O   ALA a 245 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASN a 249 " --> pdb=" O   ALA a 246 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 265 through 275
      removed outlier: 4.071A  pdb=" N   PHE a 269 " --> pdb=" O   ASP a 265 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA a 270 " --> pdb=" O   ILE a 266 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 300 through 316
      removed outlier: 3.755A  pdb=" N   HIS a 310 " --> pdb=" O   GLU a 306 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL a 311 " --> pdb=" O   SER a 307 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 354 through 364
      removed outlier: 4.012A  pdb=" N   MET a 358 " --> pdb=" O   ARG a 354 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 377 through 381
      removed outlier: 3.611A  pdb=" N   MET a 380 " --> pdb=" O   GLY a 377 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   ASN a 381 " --> pdb=" O   LYS a 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 377 through 381'
    Processing helix  chain 'a' and resid 384 through 389
      removed outlier: 3.594A  pdb=" N   LEU a 388 " --> pdb=" O   GLN a 384 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 409 through 427
      removed outlier: 4.278A  pdb=" N   PHE a 413 " --> pdb=" O   GLU a 409 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 443 through 457
    Processing helix  chain 'a' and resid 503 through 510
    Processing helix  chain 'a' and resid 513 through 518
      removed outlier: 3.624A  pdb=" N   LYS a 517 " --> pdb=" O   GLU a 513 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 520 through 529
      Proline residue:  a 526  - end of helix
      removed outlier: 4.031A  pdb=" N   PHE a 529 " --> pdb=" O   LEU a 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 75
      removed outlier: 3.692A  pdb=" N   GLY A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 82
      No H-bonds generated for 'chain 'A' and resid 80 through 82'
    Processing helix  chain 'A' and resid 98 through 107
      removed outlier: 3.602A  pdb=" N   ARG A 102 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TRP A 104 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA A 107 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 112
      removed outlier: 3.763A  pdb=" N   TYR A 112 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 157
      removed outlier: 3.773A  pdb=" N   TYR A 140 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   MET A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 182
      removed outlier: 3.535A  pdb=" N   ALA A 182 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 265 through 276
      removed outlier: 4.122A  pdb=" N   PHE A 269 " --> pdb=" O   ASP A 265 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 317
      removed outlier: 3.662A  pdb=" N   HIS A 310 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLN A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 364
      removed outlier: 4.043A  pdb=" N   ARG A 357 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   MET A 358 " --> pdb=" O   ARG A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.680A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 427
      removed outlier: 4.247A  pdb=" N   PHE A 413 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
    Processing helix  chain 'A' and resid 502 through 511
    Processing helix  chain 'A' and resid 513 through 518
      removed outlier: 4.164A  pdb=" N   LYS A 517 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 529
      Proline residue:  A 526  - end of helix
      removed outlier: 3.958A  pdb=" N   PHE A 529 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 540
      removed outlier: 3.643A  pdb=" N   ALA A 539 " --> pdb=" O   GLU A 536 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   HIS A 540 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 536 through 540'
    Processing sheet with id=AA1, first strand: chain 'a' and resid 114 through 118
      removed outlier: 4.288A  pdb=" N   SER a 114 " --> pdb=" O   THR a  84 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR a  90 " --> pdb=" O   ARG a 118 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU a  55 " --> pdb=" O   LEU a 163 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   VAL a 187 " --> pdb=" O   TYR a 281 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   CYS a 283 " --> pdb=" O   VAL a 187 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ALA a 189 " --> pdb=" O   CYS a 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 201 through 202
      removed outlier: 3.594A  pdb=" N   TRP a 202 " --> pdb=" O   MET a 233 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   MET a 233 " --> pdb=" O   TRP a 202 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'a' and resid 344 through 346
      removed outlier: 3.545A  pdb=" N   MET a 345 " --> pdb=" O   ARG a 370 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   VAL a 372 " --> pdb=" O   MET a 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'a' and resid 430 through 433
      removed outlier: 7.026A  pdb=" N   TYR a 494 " --> pdb=" O   ARG a 471 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ARG a 471 " --> pdb=" O   TYR a 494 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   THR a 496 " --> pdb=" O   ARG a 469 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ARG a 469 " --> pdb=" O   THR a 496 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ALA a 498 " --> pdb=" O   VAL a 467 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   GLY a 468 " --> pdb=" O   VAL a 551 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120
      removed outlier: 8.776A  pdb=" N   ARG A 118 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   VAL A  88 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 8.338A  pdb=" N   ALA A 120 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   THR A  90 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   TRP A  87 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ILE A  56 " --> pdb=" O   TRP A  87 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   ALA A  89 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU A  58 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   ASP A  91 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A  55 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   VAL A 165 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ALA A  57 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 238 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A 187 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   CYS A 283 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ALA A 189 " --> pdb=" O   CYS A 283 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   MET A 280 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202
      removed outlier: 3.510A  pdb=" N   MET A 233 " --> pdb=" O   TRP A 202 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 371
      removed outlier: 7.030A  pdb=" N   PHE A 344 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 440
      removed outlier: 3.551A  pdb=" N   TYR A 557 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 487 through 488
      removed outlier: 6.815A  pdb=" N   GLY A 468 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ALA A 498 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    651 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2827
        1.35 -     1.48: 2245
        1.48 -     1.61: 3687
        1.61 -     1.74: 2
        1.74 -     1.87: 88
  Bond restraints: 8849
  Sorted by residual:
  bond pdb=" C4  GDU A 801 "
       pdb=" N3  GDU A 801 "
    ideal  model  delta    sigma   weight residual
    1.388  1.327  0.061 2.00e-02 2.50e+03 9.29e+00
  bond pdb=" C4  GDU a 801 "
       pdb=" N3  GDU a 801 "
    ideal  model  delta    sigma   weight residual
    1.388  1.328  0.060 2.00e-02 2.50e+03 8.94e+00
  bond pdb=" C4  GDU A 801 "
       pdb=" C5  GDU A 801 "
    ideal  model  delta    sigma   weight residual
    1.440  1.387  0.053 2.00e-02 2.50e+03 6.91e+00
  bond pdb=" C4  GDU a 801 "
       pdb=" C5  GDU a 801 "
    ideal  model  delta    sigma   weight residual
    1.440  1.389  0.051 2.00e-02 2.50e+03 6.48e+00
  bond pdb=" C2  GDU A 801 "
       pdb=" N3  GDU A 801 "
    ideal  model  delta    sigma   weight residual
    1.373  1.329  0.044 2.00e-02 2.50e+03 4.89e+00
  ... (remaining 8844 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 11481
        1.89 -     3.79: 465
        3.79 -     5.68: 53
        5.68 -     7.57: 15
        7.57 -     9.47: 5
  Bond angle restraints: 12019
  Sorted by residual:
  angle pdb=" C   PHE A 434 "
        pdb=" N   GLU A 435 "
        pdb=" CA  GLU A 435 "
      ideal   model   delta    sigma   weight residual
     122.44  116.43    6.01 1.19e+00 7.06e-01 2.55e+01
  angle pdb=" N   MET A 338 "
        pdb=" CA  MET A 338 "
        pdb=" C   MET A 338 "
      ideal   model   delta    sigma   weight residual
     114.16  107.88    6.28 1.48e+00 4.57e-01 1.80e+01
  angle pdb=" N   VAL A 108 "
        pdb=" CA  VAL A 108 "
        pdb=" C   VAL A 108 "
      ideal   model   delta    sigma   weight residual
     113.20  109.30    3.90 9.60e-01 1.09e+00 1.65e+01
  angle pdb=" N   VAL a 108 "
        pdb=" CA  VAL a 108 "
        pdb=" C   VAL a 108 "
      ideal   model   delta    sigma   weight residual
     113.20  109.60    3.60 9.60e-01 1.09e+00 1.41e+01
  angle pdb=" N   HIS a 540 "
        pdb=" CA  HIS a 540 "
        pdb=" C   HIS a 540 "
      ideal   model   delta    sigma   weight residual
     114.56  110.04    4.52 1.27e+00 6.20e-01 1.27e+01
  ... (remaining 12014 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4828
       17.76 -    35.52: 482
       35.52 -    53.27: 116
       53.27 -    71.03: 15
       71.03 -    88.79: 6
  Dihedral angle restraints: 5447
    sinusoidal: 2349
      harmonic: 3098
  Sorted by residual:
  dihedral pdb=" CA  MET A 338 "
           pdb=" C   MET A 338 "
           pdb=" N   GLY A 339 "
           pdb=" CA  GLY A 339 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.67  -29.33     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  LYS A 337 "
           pdb=" C   LYS A 337 "
           pdb=" N   MET A 338 "
           pdb=" CA  MET A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.52   27.48     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  ASP A 436 "
           pdb=" C   ASP A 436 "
           pdb=" N   ASP A 437 "
           pdb=" CA  ASP A 437 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.07  -19.93     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1049
       0.056 -    0.112: 208
       0.112 -    0.168: 21
       0.168 -    0.224: 5
       0.224 -    0.280: 3
  Chirality restraints: 1286
  Sorted by residual:
  chirality pdb=" C2' GDU A 801 "
            pdb=" C1' GDU A 801 "
            pdb=" C3' GDU A 801 "
            pdb=" O2' GDU A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.28   -2.56    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" C2' GDU a 801 "
            pdb=" C1' GDU a 801 "
            pdb=" C3' GDU a 801 "
            pdb=" O2' GDU a 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.28   -2.54    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" C1D GDU A 801 "
            pdb=" C2D GDU A 801 "
            pdb=" N1  GDU A 801 "
            pdb=" O4D GDU A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.46   -0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1283 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP a 202 "   -0.030 2.00e-02 2.50e+03   2.06e-02 1.06e+01
        pdb=" CG  TRP a 202 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 TRP a 202 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP a 202 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP a 202 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP a 202 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP a 202 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP a 202 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP a 202 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP a 202 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 202 "    0.026 2.00e-02 2.50e+03   1.89e-02 8.92e+00
        pdb=" CG  TRP A 202 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 202 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 202 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 202 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 202 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 202 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 202 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 202 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 202 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 256 "   -0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO A 257 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 257 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 257 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 64
        2.57 -     3.16: 6589
        3.16 -     3.74: 12344
        3.74 -     4.32: 16902
        4.32 -     4.90: 29067
  Nonbonded interactions: 64966
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 168 "
            pdb="MN    MN A 802 "
     model   vdw
     1.993 2.320
  nonbonded pdb=" N   GLU a 121 "
            pdb=" OE1 GLU a 121 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" O1B GDU A 801 "
            pdb="MN    MN A 802 "
     model   vdw
     2.135 2.320
  nonbonded pdb=" NH1 ARG a  61 "
            pdb=" O   HIS a  92 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OD2 ASP a  91 "
            pdb=" NE2 HIS a 142 "
     model   vdw
     2.212 3.120
  ... (remaining 64961 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'a' and resid 41 through 802)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.810
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
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      :  0.006   0.279   8850  Z= 0.279
  Angle     :  0.870  12.496  12021  Z= 0.491
  Chirality :  0.049   0.280   1286
  Planarity :  0.005   0.050   1543
  Dihedral  : 14.957  88.790   3428
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.67 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  0.65 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.25), residues: 1038
  helix: -0.70 (0.30), residues: 328
  sheet: -1.47 (0.45), residues: 139
  loop : -2.30 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG a 469 
 TYR   0.017   0.001   TYR a 288 
 PHE   0.029   0.002   PHE A 524 
 TRP   0.055   0.002   TRP a 202 
 HIS   0.004   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 8849)
  covalent geometry    : angle       0.86045 (12019)
  SS BOND              : bond        0.27895 (    1)
  SS BOND              : angle       9.97242 (    2)
  hydrogen bonds       : bond        0.23646 (  224)
  hydrogen bonds       : angle       6.70750 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.259 
Fit side-chains
REVERT: a  418 ASN cc_start: 0.8370 (m-40) cc_final: 0.8158 (m-40)
REVERT: a  436 ASP cc_start: 0.7114 (p0) cc_final: 0.6803 (p0)
REVERT: a  552 GLU cc_start: 0.7792 (tp30) cc_final: 0.7328 (tp30)
REVERT: A   95 ASP cc_start: 0.7568 (m-30) cc_final: 0.7222 (m-30)
REVERT: A  429 GLN cc_start: 0.6893 (mp10) cc_final: 0.6385 (mp10)
REVERT: A  551 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8148 (m)
  outliers start: 8
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1094
  time to fit residues: 19.5761
Evaluate side-chains
  107 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0970
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.171018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.103549 restraints weight = 10386.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.34
r_work: 0.2785 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8850  Z= 0.138
  Angle     :  0.628  12.187  12021  Z= 0.320
  Chirality :  0.044   0.213   1286
  Planarity :  0.005   0.050   1543
  Dihedral  :  7.005  55.183   1281
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.84 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.04 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.26), residues: 1038
  helix: -0.22 (0.30), residues: 324
  sheet: -1.30 (0.43), residues: 150
  loop : -2.09 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG a  61 
 TYR   0.011   0.001   TYR A 492 
 PHE   0.015   0.002   PHE A 529 
 TRP   0.034   0.002   TRP A 202 
 HIS   0.007   0.001   HIS a 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8849)
  covalent geometry    : angle       0.62535 (12019)
  SS BOND              : bond        0.02195 (    1)
  SS BOND              : angle       4.80918 (    2)
  hydrogen bonds       : bond        0.05399 (  224)
  hydrogen bonds       : angle       4.83812 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.319 
Fit side-chains
REVERT: a  370 ARG cc_start: 0.7575 (ptm160) cc_final: 0.7255 (ptm160)
REVERT: a  436 ASP cc_start: 0.7415 (p0) cc_final: 0.6967 (p0)
REVERT: a  518 MET cc_start: 0.7089 (tpp) cc_final: 0.6648 (tpp)
REVERT: A   93 ASN cc_start: 0.8585 (m-40) cc_final: 0.8330 (m-40)
REVERT: A   95 ASP cc_start: 0.8175 (m-30) cc_final: 0.7714 (m-30)
REVERT: A  392 MET cc_start: 0.5507 (mpp) cc_final: 0.3173 (tpt)
REVERT: A  429 GLN cc_start: 0.6892 (mp10) cc_final: 0.6431 (mp10)
  outliers start: 7
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1157
  time to fit residues: 17.1700
Evaluate side-chains
  105 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  346 ILE
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  543 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.170583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.099923 restraints weight = 10325.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.98
r_work: 0.2831 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8850  Z= 0.157
  Angle     :  0.642  14.683  12021  Z= 0.324
  Chirality :  0.045   0.395   1286
  Planarity :  0.005   0.046   1543
  Dihedral  :  6.964  59.913   1280
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.03 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.78 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.26), residues: 1038
  helix:  0.06 (0.30), residues: 320
  sheet: -1.15 (0.44), residues: 149
  loop : -2.11 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a  61 
 TYR   0.011   0.001   TYR a 281 
 PHE   0.021   0.002   PHE a 229 
 TRP   0.033   0.002   TRP A 202 
 HIS   0.004   0.001   HIS a 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8849)
  covalent geometry    : angle       0.63066 (12019)
  SS BOND              : bond        0.03019 (    1)
  SS BOND              : angle       9.34270 (    2)
  hydrogen bonds       : bond        0.04913 (  224)
  hydrogen bonds       : angle       4.62378 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.241 
Fit side-chains
REVERT: a  179 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8567 (mp)
REVERT: a  370 ARG cc_start: 0.7708 (ptm160) cc_final: 0.7434 (ptm160)
REVERT: a  418 ASN cc_start: 0.8489 (m-40) cc_final: 0.8182 (m-40)
REVERT: a  436 ASP cc_start: 0.7396 (p0) cc_final: 0.7049 (p0)
REVERT: a  518 MET cc_start: 0.7154 (tpp) cc_final: 0.6677 (tpp)
REVERT: A   95 ASP cc_start: 0.8102 (m-30) cc_final: 0.7600 (m-30)
REVERT: A  141 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8538 (tt0)
REVERT: A  314 GLU cc_start: 0.8291 (tp30) cc_final: 0.8061 (tp30)
REVERT: A  341 ASP cc_start: 0.7633 (m-30) cc_final: 0.7328 (m-30)
REVERT: A  380 MET cc_start: 0.5253 (mmm) cc_final: 0.4633 (tpt)
REVERT: A  392 MET cc_start: 0.5466 (mpp) cc_final: 0.3201 (tpt)
REVERT: A  429 GLN cc_start: 0.6895 (mp10) cc_final: 0.6392 (mp10)
  outliers start: 15
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1106
  time to fit residues: 16.7298
Evaluate side-chains
  104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  179 LEU
Chi-restraints excluded: chain a residue  346 ILE
Chi-restraints excluded: chain a residue  366 GLU
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  543 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.167436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.099199 restraints weight = 10393.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.24
r_work: 0.2747 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8850  Z= 0.214
  Angle     :  0.681  15.865  12021  Z= 0.342
  Chirality :  0.047   0.347   1286
  Planarity :  0.005   0.046   1543
  Dihedral  :  7.131  59.423   1280
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.09 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.20 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.26), residues: 1038
  helix:  0.09 (0.30), residues: 322
  sheet: -1.31 (0.43), residues: 150
  loop : -2.19 (0.24), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  53 
 TYR   0.011   0.002   TYR A 198 
 PHE   0.017   0.002   PHE A 238 
 TRP   0.039   0.002   TRP A 202 
 HIS   0.004   0.001   HIS a 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 8849)
  covalent geometry    : angle       0.66919 (12019)
  SS BOND              : bond        0.01900 (    1)
  SS BOND              : angle       9.81607 (    2)
  hydrogen bonds       : bond        0.05052 (  224)
  hydrogen bonds       : angle       4.58497 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: a  179 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8614 (mp)
REVERT: a  260 THR cc_start: 0.8754 (m) cc_final: 0.8374 (p)
REVERT: a  436 ASP cc_start: 0.7535 (p0) cc_final: 0.7158 (p0)
REVERT: A   93 ASN cc_start: 0.8670 (m-40) cc_final: 0.8461 (m-40)
REVERT: A   95 ASP cc_start: 0.8229 (m-30) cc_final: 0.7706 (m-30)
REVERT: A  141 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8681 (tt0)
REVERT: A  314 GLU cc_start: 0.8356 (tp30) cc_final: 0.8151 (tp30)
REVERT: A  341 ASP cc_start: 0.8032 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  380 MET cc_start: 0.5525 (mmm) cc_final: 0.4768 (tpt)
REVERT: A  429 GLN cc_start: 0.6786 (mp10) cc_final: 0.6354 (mp10)
REVERT: A  552 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7800 (tp30)
  outliers start: 28
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1057
  time to fit residues: 17.7087
Evaluate side-chains
  111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  179 LEU
Chi-restraints excluded: chain a residue  205 MET
Chi-restraints excluded: chain a residue  346 ILE
Chi-restraints excluded: chain a residue  467 VAL
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.170314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.099066 restraints weight = 10410.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.00
r_work: 0.2824 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8850  Z= 0.115
  Angle     :  0.607  16.632  12021  Z= 0.307
  Chirality :  0.045   0.405   1286
  Planarity :  0.004   0.044   1543
  Dihedral  :  6.539  59.060   1280
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.03 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.17 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.26), residues: 1038
  helix:  0.44 (0.31), residues: 315
  sheet: -1.11 (0.44), residues: 145
  loop : -2.03 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 469 
 TYR   0.009   0.001   TYR a 288 
 PHE   0.014   0.001   PHE A 529 
 TRP   0.026   0.001   TRP a 202 
 HIS   0.003   0.001   HIS a 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8849)
  covalent geometry    : angle       0.59386 (12019)
  SS BOND              : bond        0.02807 (    1)
  SS BOND              : angle       9.71424 (    2)
  hydrogen bonds       : bond        0.03945 (  224)
  hydrogen bonds       : angle       4.36193 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.234 
Fit side-chains
REVERT: a  260 THR cc_start: 0.8732 (m) cc_final: 0.8314 (p)
REVERT: a  418 ASN cc_start: 0.8446 (m-40) cc_final: 0.8129 (m110)
REVERT: a  436 ASP cc_start: 0.7442 (p0) cc_final: 0.7115 (p0)
REVERT: a  518 MET cc_start: 0.7336 (tpp) cc_final: 0.7087 (tpp)
REVERT: A   95 ASP cc_start: 0.8109 (m-30) cc_final: 0.7566 (m-30)
REVERT: A  141 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8505 (tt0)
REVERT: A  202 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.8048 (p90)
REVERT: A  341 ASP cc_start: 0.8050 (m-30) cc_final: 0.7817 (m-30)
REVERT: A  380 MET cc_start: 0.5495 (mmm) cc_final: 0.4722 (tpt)
REVERT: A  392 MET cc_start: 0.5342 (mpp) cc_final: 0.2986 (tpt)
REVERT: A  429 GLN cc_start: 0.6784 (mp10) cc_final: 0.6380 (mp10)
REVERT: A  552 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7753 (tp30)
  outliers start: 18
  outliers final: 9
  residues processed: 121
  average time/residue: 0.1042
  time to fit residues: 16.8851
Evaluate side-chains
  110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   58 LEU
Chi-restraints excluded: chain a residue  346 ILE
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  202 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 88 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0670
   chunk 85 optimal weight:    9.9990
   overall best weight:    2.3524

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

Flipped N/Q/H residues before XYZ refinement:
A 169 ASN
A 347 ASN
A 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.167822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.100227 restraints weight = 10342.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.22
r_work: 0.2705 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2568 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8850  Z= 0.210
  Angle     :  0.692  21.419  12021  Z= 0.345
  Chirality :  0.048   0.415   1286
  Planarity :  0.005   0.046   1543
  Dihedral  :  6.926  55.918   1280
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.57 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.50 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.26), residues: 1038
  helix:  0.32 (0.31), residues: 323
  sheet: -1.22 (0.44), residues: 144
  loop : -2.12 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 147 
 TYR   0.012   0.001   TYR A 198 
 PHE   0.018   0.002   PHE a 529 
 TRP   0.034   0.002   TRP A 202 
 HIS   0.004   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 8849)
  covalent geometry    : angle       0.67850 (12019)
  SS BOND              : bond        0.03322 (    1)
  SS BOND              : angle      10.71366 (    2)
  hydrogen bonds       : bond        0.04802 (  224)
  hydrogen bonds       : angle       4.47635 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.317 
Fit side-chains
REVERT: a  260 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8393 (p)
REVERT: a  418 ASN cc_start: 0.8477 (m-40) cc_final: 0.8172 (m-40)
REVERT: a  436 ASP cc_start: 0.7509 (p0) cc_final: 0.7133 (p0)
REVERT: a  518 MET cc_start: 0.7329 (tpp) cc_final: 0.6992 (tpp)
REVERT: A   93 ASN cc_start: 0.8637 (m-40) cc_final: 0.8384 (m-40)
REVERT: A   95 ASP cc_start: 0.8277 (m-30) cc_final: 0.7739 (m-30)
REVERT: A  141 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8715 (tt0)
REVERT: A  202 TRP cc_start: 0.8599 (OUTLIER) cc_final: 0.8293 (p90)
REVERT: A  341 ASP cc_start: 0.7993 (m-30) cc_final: 0.7722 (m-30)
REVERT: A  358 MET cc_start: 0.7608 (tpp) cc_final: 0.7324 (tpp)
REVERT: A  380 MET cc_start: 0.5666 (mmm) cc_final: 0.4780 (tpt)
REVERT: A  429 GLN cc_start: 0.6756 (mp10) cc_final: 0.6340 (mp10)
REVERT: A  552 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7879 (tp30)
  outliers start: 23
  outliers final: 13
  residues processed: 120
  average time/residue: 0.1059
  time to fit residues: 17.3652
Evaluate side-chains
  113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 LEU
Chi-restraints excluded: chain a residue   58 LEU
Chi-restraints excluded: chain a residue  108 VAL
Chi-restraints excluded: chain a residue  260 THR
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain a residue  543 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  202 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  474 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 90 optimal weight:   20.0000
   chunk 57 optimal weight:    7.9990
   chunk 76 optimal weight:    0.5980
   chunk 45 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0770
   overall best weight:    1.3142

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.169886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.098087 restraints weight = 10402.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.01
r_work: 0.2798 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8850  Z= 0.134
  Angle     :  0.610  14.872  12021  Z= 0.308
  Chirality :  0.044   0.338   1286
  Planarity :  0.005   0.046   1543
  Dihedral  :  6.527  55.299   1280
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.51 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.83 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.26), residues: 1038
  helix:  0.51 (0.31), residues: 321
  sheet: -1.09 (0.45), residues: 145
  loop : -2.03 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG a 370 
 TYR   0.010   0.001   TYR a 396 
 PHE   0.015   0.001   PHE a 529 
 TRP   0.028   0.001   TRP A 202 
 HIS   0.003   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8849)
  covalent geometry    : angle       0.59728 (12019)
  SS BOND              : bond        0.01920 (    1)
  SS BOND              : angle       9.65778 (    2)
  hydrogen bonds       : bond        0.04047 (  224)
  hydrogen bonds       : angle       4.35779 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.318 
Fit side-chains
REVERT: a  260 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8378 (p)
REVERT: a  345 MET cc_start: 0.8240 (tpt) cc_final: 0.7956 (tpt)
REVERT: a  418 ASN cc_start: 0.8470 (m-40) cc_final: 0.8155 (m-40)
REVERT: a  436 ASP cc_start: 0.7426 (p0) cc_final: 0.7085 (p0)
REVERT: a  518 MET cc_start: 0.7308 (tpp) cc_final: 0.7051 (tpp)
REVERT: A   93 ASN cc_start: 0.8585 (m-40) cc_final: 0.8376 (m-40)
REVERT: A   95 ASP cc_start: 0.8168 (m-30) cc_final: 0.7613 (m-30)
REVERT: A  141 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8516 (tt0)
REVERT: A  202 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.8145 (p90)
REVERT: A  318 LYS cc_start: 0.7988 (mttt) cc_final: 0.7613 (ttpt)
REVERT: A  380 MET cc_start: 0.5585 (mmm) cc_final: 0.4754 (tpt)
REVERT: A  552 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7708 (tp30)
  outliers start: 26
  outliers final: 13
  residues processed: 120
  average time/residue: 0.0981
  time to fit residues: 16.1779
Evaluate side-chains
  115 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   58 LEU
Chi-restraints excluded: chain a residue  108 VAL
Chi-restraints excluded: chain a residue  260 THR
Chi-restraints excluded: chain a residue  366 GLU
Chi-restraints excluded: chain a residue  410 LEU
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain a residue  543 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  202 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  543 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 90 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.170135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.118571 restraints weight = 10268.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.73
r_work: 0.2810 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8850  Z= 0.192
  Angle     :  0.708  24.824  12021  Z= 0.352
  Chirality :  0.047   0.414   1286
  Planarity :  0.005   0.047   1543
  Dihedral  :  6.817  53.087   1280
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.09 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.91 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.26), residues: 1038
  helix:  0.45 (0.31), residues: 322
  sheet: -1.16 (0.44), residues: 145
  loop : -2.07 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a 370 
 TYR   0.010   0.001   TYR a 396 
 PHE   0.017   0.002   PHE a 529 
 TRP   0.033   0.002   TRP A 202 
 HIS   0.004   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8849)
  covalent geometry    : angle       0.69065 (12019)
  SS BOND              : bond        0.03960 (    1)
  SS BOND              : angle      11.98426 (    2)
  hydrogen bonds       : bond        0.04619 (  224)
  hydrogen bonds       : angle       4.44992 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.278 
Fit side-chains
REVERT: a  260 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8270 (p)
REVERT: a  345 MET cc_start: 0.8150 (tpt) cc_final: 0.7875 (tpt)
REVERT: a  418 ASN cc_start: 0.8461 (m-40) cc_final: 0.8147 (m-40)
REVERT: a  436 ASP cc_start: 0.7306 (p0) cc_final: 0.6998 (p0)
REVERT: a  518 MET cc_start: 0.7371 (tpp) cc_final: 0.7059 (tpp)
REVERT: A   95 ASP cc_start: 0.8083 (m-30) cc_final: 0.7528 (m-30)
REVERT: A  141 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8429 (tt0)
REVERT: A  202 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.8272 (p90)
REVERT: A  318 LYS cc_start: 0.7901 (mttt) cc_final: 0.7508 (ttpt)
REVERT: A  341 ASP cc_start: 0.7650 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  380 MET cc_start: 0.5620 (mmm) cc_final: 0.4751 (tpt)
REVERT: A  429 GLN cc_start: 0.6744 (mp10) cc_final: 0.6451 (mp10)
  outliers start: 19
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1076
  time to fit residues: 17.0007
Evaluate side-chains
  116 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   58 LEU
Chi-restraints excluded: chain a residue  108 VAL
Chi-restraints excluded: chain a residue  260 THR
Chi-restraints excluded: chain a residue  410 LEU
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain a residue  543 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  202 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0470
   chunk 40 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 100 optimal weight:   10.0000
   chunk 73 optimal weight:    0.0570
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.172259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.101264 restraints weight = 10225.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.00
r_work: 0.2853 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8850  Z= 0.097
  Angle     :  0.610  20.931  12021  Z= 0.307
  Chirality :  0.044   0.377   1286
  Planarity :  0.004   0.045   1543
  Dihedral  :  6.162  51.859   1280
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.84 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.02 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.26), residues: 1038
  helix:  0.78 (0.31), residues: 320
  sheet: -1.10 (0.45), residues: 137
  loop : -1.91 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a 370 
 TYR   0.009   0.001   TYR a 396 
 PHE   0.014   0.001   PHE a 529 
 TRP   0.020   0.001   TRP A 202 
 HIS   0.003   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8849)
  covalent geometry    : angle       0.59255 (12019)
  SS BOND              : bond        0.02467 (    1)
  SS BOND              : angle      11.39876 (    2)
  hydrogen bonds       : bond        0.03468 (  224)
  hydrogen bonds       : angle       4.26747 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.315 
Fit side-chains
REVERT: a  260 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8319 (p)
REVERT: a  436 ASP cc_start: 0.7216 (p0) cc_final: 0.6937 (p0)
REVERT: a  518 MET cc_start: 0.7314 (tpp) cc_final: 0.7092 (tpp)
REVERT: A   95 ASP cc_start: 0.8077 (m-30) cc_final: 0.7454 (m-30)
REVERT: A  141 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8437 (tt0)
REVERT: A  202 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.8053 (p90)
REVERT: A  318 LYS cc_start: 0.7916 (mttt) cc_final: 0.7555 (ttpt)
REVERT: A  341 ASP cc_start: 0.7725 (m-30) cc_final: 0.7492 (m-30)
REVERT: A  380 MET cc_start: 0.5584 (mmm) cc_final: 0.4704 (tpt)
REVERT: A  392 MET cc_start: 0.5569 (mpp) cc_final: 0.3346 (tmm)
REVERT: A  409 GLU cc_start: 0.6784 (tt0) cc_final: 0.6523 (tt0)
REVERT: A  429 GLN cc_start: 0.6790 (mp10) cc_final: 0.6496 (mp10)
  outliers start: 16
  outliers final: 9
  residues processed: 123
  average time/residue: 0.1014
  time to fit residues: 17.0814
Evaluate side-chains
  113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  108 VAL
Chi-restraints excluded: chain a residue  260 THR
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  202 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  543 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 86 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.170159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.101483 restraints weight = 10241.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.97
r_work: 0.2858 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8850  Z= 0.155
  Angle     :  0.654  21.244  12021  Z= 0.326
  Chirality :  0.045   0.375   1286
  Planarity :  0.005   0.044   1543
  Dihedral  :  6.467  50.572   1280
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.57 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.26), residues: 1038
  helix:  0.72 (0.31), residues: 322
  sheet: -1.02 (0.45), residues: 143
  loop : -2.00 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG a 370 
 TYR   0.010   0.001   TYR a 396 
 PHE   0.016   0.001   PHE a 529 
 TRP   0.028   0.001   TRP A 202 
 HIS   0.003   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8849)
  covalent geometry    : angle       0.63743 (12019)
  SS BOND              : bond        0.02882 (    1)
  SS BOND              : angle      11.32954 (    2)
  hydrogen bonds       : bond        0.04112 (  224)
  hydrogen bonds       : angle       4.31878 (  651)

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.344 
Fit side-chains
REVERT: a  260 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8349 (p)
REVERT: a  436 ASP cc_start: 0.7222 (p0) cc_final: 0.6912 (p0)
REVERT: a  518 MET cc_start: 0.7340 (tpp) cc_final: 0.7068 (tpp)
REVERT: A   95 ASP cc_start: 0.8129 (m-30) cc_final: 0.7551 (m-30)
REVERT: A  141 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (tt0)
REVERT: A  202 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.8123 (p90)
REVERT: A  318 LYS cc_start: 0.8025 (mttt) cc_final: 0.7664 (ttpt)
REVERT: A  380 MET cc_start: 0.5588 (mmm) cc_final: 0.4697 (tpt)
REVERT: A  409 GLU cc_start: 0.6778 (tt0) cc_final: 0.6500 (tt0)
  outliers start: 14
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1132
  time to fit residues: 16.3546
Evaluate side-chains
  108 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  108 VAL
Chi-restraints excluded: chain a residue  260 THR
Chi-restraints excluded: chain a residue  346 ILE
Chi-restraints excluded: chain a residue  410 LEU
Chi-restraints excluded: chain a residue  474 VAL
Chi-restraints excluded: chain a residue  521 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  202 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0020
   chunk 31 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.171381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.102156 restraints weight = 10275.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.91
r_work: 0.2861 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8850  Z= 0.117
  Angle     :  0.620  19.899  12021  Z= 0.311
  Chirality :  0.044   0.361   1286
  Planarity :  0.004   0.044   1543
  Dihedral  :  6.277  50.009   1280
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.67 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.26), residues: 1038
  helix:  0.88 (0.31), residues: 320
  sheet: -1.06 (0.45), residues: 137
  loop : -1.90 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a 370 
 TYR   0.009   0.001   TYR a 396 
 PHE   0.015   0.001   PHE a 529 
 TRP   0.024   0.001   TRP A 202 
 HIS   0.003   0.001   HIS a 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8849)
  covalent geometry    : angle       0.60299 (12019)
  SS BOND              : bond        0.02597 (    1)
  SS BOND              : angle      11.08400 (    2)
  hydrogen bonds       : bond        0.03777 (  224)
  hydrogen bonds       : angle       4.25174 (  651)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2957.84 seconds
wall clock time: 51 minutes 4.32 seconds (3064.32 seconds total)