Starting phenix.real_space_refine
on Tue Mar  3 18:20:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsp_32763/03_2026/7wsp_32763.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsp_32763/03_2026/7wsp_32763.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsp_32763/03_2026/7wsp_32763.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsp_32763/03_2026/7wsp_32763.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsp_32763/03_2026/7wsp_32763.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsp_32763/03_2026/7wsp_32763.cif"
  }
  resolution = 4.09
  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=   0.003 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4993      2.51       5
     N    1344      2.21       5
     O    1506      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7883
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1076
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1128
          Classifications: {'peptide': 139}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135}
    Chain: "B"
      Number of atoms: 2837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2837
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 339}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 2842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2842
          Classifications: {'peptide': 367}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 341}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 1.76, per 1000 atoms: 0.22
  Number of scatterers: 7883
  At special positions: 0
  Unit cell: (68.2, 104.5, 192.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1506      8.00
     N    1344      7.00
     C    4993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 106 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS C 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 122 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 270 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS D 350 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 380 " - pdb=" SG  CYS B 439 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 487 " - pdb=" SG  CYS B 549 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 270 " - pdb=" SG  CYS D 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 380 " - pdb=" SG  CYS D 439 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 487 " - pdb=" SG  CYS D 549 " distance=2.05

  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: 0.66
  Conformation dependent library (CDL) restraints added in 295.5 milliseconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 21 sheets defined
      18.2% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 166
      removed outlier: 4.214A  pdb=" N   ARG A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   VAL A 158 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
      removed outlier: 3.913A  pdb=" N   LEU A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.846A  pdb=" N   ASN C 117 " --> pdb=" O   PHE C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 181
      removed outlier: 3.811A  pdb=" N   LYS C 152 " --> pdb=" O   LEU C 148 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      Proline residue:  C 176  - end of helix
    Processing helix  chain 'B' and resid 322 through 326
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.992A  pdb=" N   TRP B 431 " --> pdb=" O   CYS B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479
      removed outlier: 3.959A  pdb=" N   ASN B 478 " --> pdb=" O   ARG B 474 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 479 " --> pdb=" O   GLU B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 542
      removed outlier: 3.717A  pdb=" N   TRP B 541 " --> pdb=" O   SER B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 607
      removed outlier: 3.735A  pdb=" N   TRP B 584 " --> pdb=" O   PHE B 580 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE B 599 " --> pdb=" O   LEU B 595 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   TYR B 600 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   THR B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL B 604 " --> pdb=" O   TYR B 600 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 327
    Processing helix  chain 'D' and resid 368 through 374
      removed outlier: 4.135A  pdb=" N   LEU D 372 " --> pdb=" O   ALA D 368 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   THR D 373 " --> pdb=" O   SER D 369 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 480
    Processing helix  chain 'D' and resid 537 through 542
    Processing helix  chain 'D' and resid 575 through 607
      removed outlier: 3.989A  pdb=" N   THR D 605 " --> pdb=" O   SER D 601 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44
      removed outlier: 3.944A  pdb=" N   ARG A 124 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL A  44 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 83
      removed outlier: 4.016A  pdb=" N   GLU A  79 " --> pdb=" O   ARG A  68 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG A  68 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   TRP A  66 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   VAL A  64 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 103 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 49
      removed outlier: 3.558A  pdb=" N   VAL C  61 " --> pdb=" O   ILE C 109 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE C 109 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU C 107 " --> pdb=" O   MET C  63 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA C 105 " --> pdb=" O   CYS C  65 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU C 104 " --> pdb=" O   ASN C 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 56
      removed outlier: 6.485A  pdb=" N   ILE C  53 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   MET C 143 " --> pdb=" O   ILE C  53 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ARG C  55 " --> pdb=" O   MET C 143 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88
      removed outlier: 3.802A  pdb=" N   TRP C  78 " --> pdb=" O   GLN C  87 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 252
      removed outlier: 4.186A  pdb=" N   ILE B 269 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS B 270 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER B 316 " --> pdb=" O   CYS B 270 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA B 272 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL B 314 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   TYR B 312 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 252
      removed outlier: 4.186A  pdb=" N   ILE B 269 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS B 270 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER B 316 " --> pdb=" O   CYS B 270 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA B 272 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL B 314 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   TYR B 312 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 290
      removed outlier: 3.520A  pdb=" N   CYS B 333 " --> pdb=" O   GLN B 344 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 381 through 385
      removed outlier: 3.599A  pdb=" N   VAL B 382 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 396
      removed outlier: 3.794A  pdb=" N   THR B 440 " --> pdb=" O   SER B 394 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 466 through 470
      removed outlier: 3.608A  pdb=" N   ASP B 466 " --> pdb=" O   THR B 490 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 490 " --> pdb=" O   ASP B 466 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR B 486 " --> pdb=" O   LEU B 470 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER B 532 " --> pdb=" O   CYS B 487 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL B 489 " --> pdb=" O   ALA B 530 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR B 528 " --> pdb=" O   GLY B 491 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 506 through 507
      removed outlier: 3.798A  pdb=" N   GLN B 503 " --> pdb=" O   GLN B 506 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN B 500 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 252
      removed outlier: 4.122A  pdb=" N   THR D 273 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ILE D 269 " --> pdb=" O   PHE D 252 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ILE D 269 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU D 318 " --> pdb=" O   ILE D 269 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLN D 271 " --> pdb=" O   SER D 316 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   SER D 316 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   THR D 273 " --> pdb=" O   VAL D 314 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL D 314 " --> pdb=" O   THR D 273 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 248 through 252
      removed outlier: 4.122A  pdb=" N   THR D 273 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ILE D 269 " --> pdb=" O   PHE D 252 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ILE D 269 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU D 318 " --> pdb=" O   ILE D 269 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLN D 271 " --> pdb=" O   SER D 316 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   SER D 316 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   THR D 273 " --> pdb=" O   VAL D 314 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL D 314 " --> pdb=" O   THR D 273 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 266
    Processing sheet with id=AB7, first strand: chain 'D' and resid 281 through 283
      removed outlier: 3.587A  pdb=" N   HIS D 337 " --> pdb=" O   LEU D 340 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 331 through 332
    Processing sheet with id=AB9, first strand: chain 'D' and resid 360 through 362
      removed outlier: 3.564A  pdb=" N   GLY D 422 " --> pdb=" O   CYS D 380 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 392 through 396
    Processing sheet with id=AC2, first strand: chain 'D' and resid 466 through 470
      removed outlier: 3.526A  pdb=" N   ASP D 466 " --> pdb=" O   THR D 490 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU D 488 " --> pdb=" O   TYR D 468 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR D 486 " --> pdb=" O   LEU D 470 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   TYR D 528 " --> pdb=" O   GLY D 491 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 501 through 502

    245 hydrogen bonds defined for protein.
    642 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: 1.16

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2477
        1.34 -     1.46: 1954
        1.46 -     1.59: 3589
        1.59 -     1.71: 0
        1.71 -     1.84: 56
  Bond restraints: 8076
  Sorted by residual:
  bond pdb=" C   VAL D 351 "
       pdb=" N   PRO D 352 "
    ideal  model  delta    sigma   weight residual
    1.330  1.366 -0.036 1.19e-02 7.06e+03 8.96e+00
  bond pdb=" CA  TYR D 468 "
       pdb=" CB  TYR D 468 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.75e-02 3.27e+03 8.08e+00
  bond pdb=" CB  TRP C  47 "
       pdb=" CG  TRP C  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.431  0.067 3.10e-02 1.04e+03 4.63e+00
  bond pdb=" CB  VAL C 142 "
       pdb=" CG2 VAL C 142 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.77e+00
  bond pdb=" CB  PHE D 594 "
       pdb=" CG  PHE D 594 "
    ideal  model  delta    sigma   weight residual
    1.502  1.459  0.043 2.30e-02 1.89e+03 3.46e+00
  ... (remaining 8071 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 10379
        2.18 -     4.36: 526
        4.36 -     6.54: 69
        6.54 -     8.73: 22
        8.73 -    10.91: 9
  Bond angle restraints: 11005
  Sorted by residual:
  angle pdb=" C   ASP A 135 "
        pdb=" N   MET A 136 "
        pdb=" CA  MET A 136 "
      ideal   model   delta    sigma   weight residual
     121.54  132.17  -10.63 1.91e+00 2.74e-01 3.10e+01
  angle pdb=" C   GLU D 545 "
        pdb=" N   THR D 546 "
        pdb=" CA  THR D 546 "
      ideal   model   delta    sigma   weight residual
     121.54  131.29   -9.75 1.91e+00 2.74e-01 2.61e+01
  angle pdb=" N   VAL A 158 "
        pdb=" CA  VAL A 158 "
        pdb=" C   VAL A 158 "
      ideal   model   delta    sigma   weight residual
     108.88  119.79  -10.91 2.16e+00 2.14e-01 2.55e+01
  angle pdb=" N   GLU B 570 "
        pdb=" CA  GLU B 570 "
        pdb=" C   GLU B 570 "
      ideal   model   delta    sigma   weight residual
     110.80  100.66   10.14 2.13e+00 2.20e-01 2.27e+01
  angle pdb=" C   LEU A  70 "
        pdb=" N   HIS A  71 "
        pdb=" CA  HIS A  71 "
      ideal   model   delta    sigma   weight residual
     121.19  128.51   -7.32 1.59e+00 3.96e-01 2.12e+01
  ... (remaining 11000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.52: 4494
       15.52 -    31.04: 283
       31.04 -    46.56: 76
       46.56 -    62.07: 6
       62.07 -    77.59: 2
  Dihedral angle restraints: 4861
    sinusoidal: 1937
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" CA  VAL D 351 "
           pdb=" C   VAL D 351 "
           pdb=" N   PRO D 352 "
           pdb=" CA  PRO D 352 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.04  -48.96     0      5.00e+00 4.00e-02 9.59e+01
  dihedral pdb=" CA  GLN A 127 "
           pdb=" C   GLN A 127 "
           pdb=" N   PRO A 128 "
           pdb=" CA  PRO A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.05  -43.95     0      5.00e+00 4.00e-02 7.73e+01
  dihedral pdb=" CA  GLU B 577 "
           pdb=" C   GLU B 577 "
           pdb=" N   GLU B 578 "
           pdb=" CA  GLU B 578 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.80  -39.20     0      5.00e+00 4.00e-02 6.15e+01
  ... (remaining 4858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1073
       0.089 -    0.179: 168
       0.179 -    0.268: 12
       0.268 -    0.358: 0
       0.358 -    0.447: 1
  Chirality restraints: 1254
  Sorted by residual:
  chirality pdb=" CB  ILE B 358 "
            pdb=" CA  ILE B 358 "
            pdb=" CG1 ILE B 358 "
            pdb=" CG2 ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.45 2.00e-01 2.50e+01 5.00e+00
  chirality pdb=" CB  VAL B 497 "
            pdb=" CA  VAL B 497 "
            pdb=" CG1 VAL B 497 "
            pdb=" CG2 VAL B 497 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A  38 "
            pdb=" CA  VAL A  38 "
            pdb=" CG1 VAL A  38 "
            pdb=" CG2 VAL A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1251 not shown)

  Planarity restraints: 1419
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 509 "   -0.052 5.00e-02 4.00e+02   7.81e-02 9.76e+00
        pdb=" N   PRO B 510 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 510 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 510 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 577 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.48e+00
        pdb=" C   GLU B 577 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLU B 577 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B 578 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 413 "   -0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO D 414 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO D 414 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 414 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1416 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1021
        2.75 -     3.29: 7339
        3.29 -     3.82: 12572
        3.82 -     4.36: 13578
        4.36 -     4.90: 23414
  Nonbonded interactions: 57924
  Sorted by model distance:
  nonbonded pdb=" O   THR D 546 "
            pdb=" OG1 THR D 564 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   PHE D 599 "
            pdb=" OG1 THR D 603 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG1 THR B 396 "
            pdb=" OG1 THR B 438 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   MET B 502 "
            pdb=" OG1 THR B 548 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU D 583 "
            pdb=" OG1 THR D 586 "
     model   vdw
     2.272 3.040
  ... (remaining 57919 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 'B' and (resid 242 through 352 or (resid 353 through 355 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 356 through 357 or (resid 358  \ 
and (name N or name CA or name C or name O or name CB )) or resid 359 through 60 \ 
7))
  selection = (chain 'D' and (resid 242 through 255 or (resid 256 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 257 through 348 or (resid 349 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 350 through 607))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.280
  Find NCS groups from input model:        0.090
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
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      :  0.008   0.085   8086  Z= 0.352
  Angle     :  1.118  10.908  11025  Z= 0.602
  Chirality :  0.062   0.447   1254
  Planarity :  0.008   0.078   1419
  Dihedral  : 10.989  77.592   2933
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.19 %
    Favored  : 86.61 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.75 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.43 %

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: -4.84 (0.21), residues: 1001
  helix: -3.07 (0.27), residues: 156
  sheet: -3.04 (0.30), residues: 240
  loop : -3.48 (0.21), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 359 
 TYR   0.037   0.004   TYR C  66 
 PHE   0.026   0.003   PHE C 145 
 TRP   0.024   0.003   TRP D 541 
 HIS   0.013   0.003   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00796 ( 8076)
  covalent geometry    : angle       1.11473 (11005)
  SS BOND              : bond        0.01157 (   10)
  SS BOND              : angle       2.33423 (   20)
  hydrogen bonds       : bond        0.25357 (  233)
  hydrogen bonds       : angle      11.19371 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 MET cc_start: 0.7860 (mtt) cc_final: 0.7251 (mtt)
REVERT: B  502 MET cc_start: 0.7947 (mmm) cc_final: 0.7654 (mtm)
REVERT: D  395 TRP cc_start: 0.8311 (m100) cc_final: 0.7553 (m100)
REVERT: D  513 TYR cc_start: 0.7339 (p90) cc_final: 0.6647 (p90)
  outliers start: 6
  outliers final: 2
  residues processed: 147
  average time/residue: 0.0888
  time to fit residues: 17.7038
Evaluate side-chains
  81 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.0670
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:   40.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
B 406 HIS
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 271 GLN
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.128170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.097614 restraints weight = 23625.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.095641 restraints weight = 22184.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.096176 restraints weight = 23951.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.096366 restraints weight = 15877.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.097388 restraints weight = 13688.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8086  Z= 0.145
  Angle     :  0.741   9.193  11025  Z= 0.386
  Chirality :  0.047   0.186   1254
  Planarity :  0.006   0.057   1419
  Dihedral  :  6.563  32.392   1074
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.69 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.11 %

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: -4.04 (0.23), residues: 1001
  helix: -1.47 (0.33), residues: 177
  sheet: -2.54 (0.30), residues: 259
  loop : -3.27 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 359 
 TYR   0.014   0.001   TYR C  66 
 PHE   0.015   0.001   PHE D 580 
 TRP   0.010   0.001   TRP D 541 
 HIS   0.004   0.001   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8076)
  covalent geometry    : angle       0.73668 (11005)
  SS BOND              : bond        0.00589 (   10)
  SS BOND              : angle       2.04247 (   20)
  hydrogen bonds       : bond        0.05066 (  233)
  hydrogen bonds       : angle       7.16895 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 MET cc_start: 0.7627 (mtt) cc_final: 0.7285 (mtt)
REVERT: B  502 MET cc_start: 0.7510 (mmm) cc_final: 0.6646 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0897
  time to fit residues: 13.1746
Evaluate side-chains
  71 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0870
   chunk 73 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.5762

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 HIS
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.127265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.084929 restraints weight = 22819.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.084637 restraints weight = 16791.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.084160 restraints weight = 15167.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.084884 restraints weight = 14826.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.084885 restraints weight = 13006.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8086  Z= 0.157
  Angle     :  0.707   7.911  11025  Z= 0.365
  Chirality :  0.045   0.181   1254
  Planarity :  0.005   0.048   1419
  Dihedral  :  6.063  30.077   1074
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -3.51 (0.24), residues: 1001
  helix: -0.76 (0.36), residues: 177
  sheet: -2.39 (0.30), residues: 258
  loop : -2.92 (0.24), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 359 
 TYR   0.015   0.002   TYR C  66 
 PHE   0.019   0.001   PHE D 580 
 TRP   0.014   0.001   TRP D 584 
 HIS   0.006   0.001   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8076)
  covalent geometry    : angle       0.70426 (11005)
  SS BOND              : bond        0.00856 (   10)
  SS BOND              : angle       1.69882 (   20)
  hydrogen bonds       : bond        0.04535 (  233)
  hydrogen bonds       : angle       6.49371 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   67 MET cc_start: 0.6294 (pmm) cc_final: 0.5986 (pmm)
REVERT: C   96 MET cc_start: 0.7702 (mtt) cc_final: 0.7261 (mtt)
REVERT: C  163 MET cc_start: 0.9016 (mmp) cc_final: 0.8785 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0798
  time to fit residues: 10.6635
Evaluate side-chains
  65 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 62 optimal weight:   30.0000
   chunk 14 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 HIS
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 343 GLN
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.126498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.084406 restraints weight = 22920.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.083686 restraints weight = 17668.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.083951 restraints weight = 14759.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.084656 restraints weight = 13677.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.084566 restraints weight = 12815.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8086  Z= 0.176
  Angle     :  0.698   9.442  11025  Z= 0.360
  Chirality :  0.045   0.190   1254
  Planarity :  0.005   0.048   1419
  Dihedral  :  5.889  28.600   1074
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.89 %
    Favored  : 87.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -3.22 (0.25), residues: 1001
  helix: -0.41 (0.37), residues: 177
  sheet: -2.07 (0.31), residues: 258
  loop : -2.84 (0.24), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 126 
 TYR   0.016   0.001   TYR C  66 
 PHE   0.018   0.002   PHE B 594 
 TRP   0.016   0.001   TRP D 584 
 HIS   0.008   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8076)
  covalent geometry    : angle       0.69500 (11005)
  SS BOND              : bond        0.00529 (   10)
  SS BOND              : angle       1.63937 (   20)
  hydrogen bonds       : bond        0.04364 (  233)
  hydrogen bonds       : angle       6.17670 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8710 (mm) cc_final: 0.8482 (mm)
REVERT: B  446 LEU cc_start: 0.8013 (tp) cc_final: 0.7722 (tp)
REVERT: D  599 PHE cc_start: 0.8706 (t80) cc_final: 0.8389 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0761
  time to fit residues: 9.7160
Evaluate side-chains
  66 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 81 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0870
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.9562

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS
A  94 GLN
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 343 GLN
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.127833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.085885 restraints weight = 22395.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.085270 restraints weight = 17718.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.085594 restraints weight = 14646.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.086132 restraints weight = 14017.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.086106 restraints weight = 12665.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8086  Z= 0.121
  Angle     :  0.648   7.363  11025  Z= 0.334
  Chirality :  0.044   0.175   1254
  Planarity :  0.005   0.049   1419
  Dihedral  :  5.519  26.475   1074
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.39 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.92 (0.25), residues: 1001
  helix: -0.06 (0.37), residues: 177
  sheet: -1.85 (0.32), residues: 254
  loop : -2.70 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 359 
 TYR   0.012   0.001   TYR C  66 
 PHE   0.016   0.001   PHE B 594 
 TRP   0.020   0.001   TRP D 584 
 HIS   0.003   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8076)
  covalent geometry    : angle       0.64626 (11005)
  SS BOND              : bond        0.00436 (   10)
  SS BOND              : angle       1.19142 (   20)
  hydrogen bonds       : bond        0.03791 (  233)
  hydrogen bonds       : angle       5.75730 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLN cc_start: 0.7960 (tt0) cc_final: 0.7606 (tm-30)
REVERT: A  131 ARG cc_start: 0.7123 (tmm-80) cc_final: 0.6523 (tmt170)
REVERT: A  144 ILE cc_start: 0.8755 (mm) cc_final: 0.8513 (mm)
REVERT: C   67 MET cc_start: 0.6534 (pmm) cc_final: 0.6295 (pmm)
REVERT: B  446 LEU cc_start: 0.8039 (tp) cc_final: 0.7770 (tp)
REVERT: D  599 PHE cc_start: 0.8748 (t80) cc_final: 0.8385 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0816
  time to fit residues: 10.7932
Evaluate side-chains
  68 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0670
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
A 142 ASN
B 443 HIS
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.129000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.087501 restraints weight = 22533.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.087221 restraints weight = 16657.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.087419 restraints weight = 13687.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.087947 restraints weight = 12587.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.088323 restraints weight = 11509.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8086  Z= 0.111
  Angle     :  0.638  10.842  11025  Z= 0.325
  Chirality :  0.044   0.264   1254
  Planarity :  0.005   0.051   1419
  Dihedral  :  5.291  25.444   1074
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.09 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.63 (0.26), residues: 1001
  helix:  0.16 (0.37), residues: 179
  sheet: -1.44 (0.33), residues: 250
  loop : -2.63 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 359 
 TYR   0.009   0.001   TYR C  66 
 PHE   0.023   0.001   PHE B 594 
 TRP   0.020   0.001   TRP D 584 
 HIS   0.006   0.001   HIS D 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8076)
  covalent geometry    : angle       0.63585 (11005)
  SS BOND              : bond        0.00431 (   10)
  SS BOND              : angle       1.35791 (   20)
  hydrogen bonds       : bond        0.03480 (  233)
  hydrogen bonds       : angle       5.47162 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLN cc_start: 0.7907 (tt0) cc_final: 0.7661 (tm-30)
REVERT: A  131 ARG cc_start: 0.7294 (tmm-80) cc_final: 0.6368 (tmt170)
REVERT: A  144 ILE cc_start: 0.8679 (mm) cc_final: 0.8405 (mm)
REVERT: C   67 MET cc_start: 0.6675 (pmm) cc_final: 0.6365 (pmm)
REVERT: B  446 LEU cc_start: 0.7922 (tp) cc_final: 0.7650 (tp)
REVERT: B  502 MET cc_start: 0.7819 (mtp) cc_final: 0.7152 (mtm)
REVERT: D  599 PHE cc_start: 0.8694 (t80) cc_final: 0.8338 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0769
  time to fit residues: 10.4073
Evaluate side-chains
  64 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 71 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 52 optimal weight:    0.1980
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 165 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.128274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.086096 restraints weight = 21935.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.087021 restraints weight = 15631.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.086592 restraints weight = 12032.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.087386 restraints weight = 12374.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.087320 restraints weight = 11062.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8086  Z= 0.151
  Angle     :  0.661   9.070  11025  Z= 0.339
  Chirality :  0.044   0.232   1254
  Planarity :  0.005   0.050   1419
  Dihedral  :  5.341  26.170   1074
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.57 (0.26), residues: 1001
  helix:  0.31 (0.37), residues: 180
  sheet: -1.44 (0.33), residues: 250
  loop : -2.62 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 126 
 TYR   0.021   0.002   TYR B 388 
 PHE   0.020   0.001   PHE B 594 
 TRP   0.015   0.001   TRP D 584 
 HIS   0.005   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8076)
  covalent geometry    : angle       0.65878 (11005)
  SS BOND              : bond        0.00524 (   10)
  SS BOND              : angle       1.29767 (   20)
  hydrogen bonds       : bond        0.03720 (  233)
  hydrogen bonds       : angle       5.47159 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7437 (tmm-80) cc_final: 0.6495 (tmt170)
REVERT: A  144 ILE cc_start: 0.8742 (mm) cc_final: 0.8450 (mm)
REVERT: C   67 MET cc_start: 0.6647 (pmm) cc_final: 0.6306 (pmm)
REVERT: C  113 ARG cc_start: 0.7333 (ptt180) cc_final: 0.6914 (ptt90)
REVERT: B  446 LEU cc_start: 0.7989 (tp) cc_final: 0.7696 (tp)
REVERT: B  502 MET cc_start: 0.7660 (mtp) cc_final: 0.7126 (mtm)
REVERT: D  599 PHE cc_start: 0.8770 (t80) cc_final: 0.8414 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0857
  time to fit residues: 11.3260
Evaluate side-chains
  69 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 95 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
C 165 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.127060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.082633 restraints weight = 22384.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.084372 restraints weight = 16487.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.084066 restraints weight = 11960.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.084545 restraints weight = 12948.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.084432 restraints weight = 11953.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8086  Z= 0.191
  Angle     :  0.697   8.616  11025  Z= 0.357
  Chirality :  0.045   0.219   1254
  Planarity :  0.005   0.046   1419
  Dihedral  :  5.499  27.585   1074
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.09 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.57 (0.26), residues: 1001
  helix:  0.49 (0.37), residues: 174
  sheet: -1.49 (0.33), residues: 249
  loop : -2.63 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 359 
 TYR   0.015   0.002   TYR C  66 
 PHE   0.023   0.002   PHE B 594 
 TRP   0.012   0.002   TRP C  78 
 HIS   0.007   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 8076)
  covalent geometry    : angle       0.69478 (11005)
  SS BOND              : bond        0.00630 (   10)
  SS BOND              : angle       1.48780 (   20)
  hydrogen bonds       : bond        0.03984 (  233)
  hydrogen bonds       : angle       5.60872 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7356 (tmm-80) cc_final: 0.6429 (tmt170)
REVERT: A  144 ILE cc_start: 0.8801 (mm) cc_final: 0.8492 (mm)
REVERT: C   67 MET cc_start: 0.6714 (pmm) cc_final: 0.6459 (pmm)
REVERT: C  113 ARG cc_start: 0.7500 (ptt180) cc_final: 0.7068 (ptt90)
REVERT: B  446 LEU cc_start: 0.8162 (tp) cc_final: 0.7881 (tp)
REVERT: B  502 MET cc_start: 0.7916 (mtp) cc_final: 0.7320 (mtm)
REVERT: D  599 PHE cc_start: 0.8841 (t80) cc_final: 0.8530 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0866
  time to fit residues: 10.8425
Evaluate side-chains
  67 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 69 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.125775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.079778 restraints weight = 21902.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.081612 restraints weight = 14890.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.083017 restraints weight = 11623.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.083739 restraints weight = 9904.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.084205 restraints weight = 8999.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   8086  Z= 0.238
  Angle     :  0.746   8.849  11025  Z= 0.385
  Chirality :  0.047   0.214   1254
  Planarity :  0.005   0.050   1419
  Dihedral  :  5.754  27.487   1074
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.79 %
    Favored  : 88.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.68 (0.25), residues: 1001
  helix:  0.39 (0.37), residues: 174
  sheet: -1.57 (0.33), residues: 245
  loop : -2.68 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 436 
 TYR   0.017   0.002   TYR C  66 
 PHE   0.028   0.002   PHE B 594 
 TRP   0.028   0.002   TRP D 584 
 HIS   0.009   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 8076)
  covalent geometry    : angle       0.74381 (11005)
  SS BOND              : bond        0.00709 (   10)
  SS BOND              : angle       1.44595 (   20)
  hydrogen bonds       : bond        0.04426 (  233)
  hydrogen bonds       : angle       5.78676 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.7226 (tpt) cc_final: 0.6582 (tpt)
REVERT: A  131 ARG cc_start: 0.7434 (tmm-80) cc_final: 0.6823 (tmt170)
REVERT: A  144 ILE cc_start: 0.8782 (mm) cc_final: 0.8454 (mm)
REVERT: C  113 ARG cc_start: 0.7497 (ptt180) cc_final: 0.7129 (ptt90)
REVERT: B  446 LEU cc_start: 0.8159 (tp) cc_final: 0.7356 (pt)
REVERT: B  502 MET cc_start: 0.8081 (mtp) cc_final: 0.7531 (mtm)
REVERT: D  599 PHE cc_start: 0.8686 (t80) cc_final: 0.8390 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0872
  time to fit residues: 10.6187
Evaluate side-chains
  67 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:   30.0000
   chunk 95 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 80 optimal weight:   20.0000
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
C 165 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.126934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.082236 restraints weight = 21803.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.084338 restraints weight = 15291.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.085632 restraints weight = 12065.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.085873 restraints weight = 10525.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.085984 restraints weight = 9767.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8086  Z= 0.165
  Angle     :  0.693   9.460  11025  Z= 0.355
  Chirality :  0.045   0.213   1254
  Planarity :  0.005   0.046   1419
  Dihedral  :  5.565  27.784   1074
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.49 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.56 (0.26), residues: 1001
  helix:  0.60 (0.38), residues: 174
  sheet: -1.48 (0.33), residues: 241
  loop : -2.65 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 124 
 TYR   0.014   0.001   TYR B 388 
 PHE   0.018   0.002   PHE B 594 
 TRP   0.040   0.002   TRP D 584 
 HIS   0.006   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8076)
  covalent geometry    : angle       0.69143 (11005)
  SS BOND              : bond        0.00511 (   10)
  SS BOND              : angle       1.18739 (   20)
  hydrogen bonds       : bond        0.04056 (  233)
  hydrogen bonds       : angle       5.58045 (  642)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7506 (tmm-80) cc_final: 0.6794 (tmt170)
REVERT: A  144 ILE cc_start: 0.8767 (mm) cc_final: 0.8441 (mm)
REVERT: C  113 ARG cc_start: 0.7385 (ptt180) cc_final: 0.7027 (ptt90)
REVERT: B  446 LEU cc_start: 0.8073 (tp) cc_final: 0.7266 (pt)
REVERT: B  502 MET cc_start: 0.7894 (mtp) cc_final: 0.7338 (mtm)
REVERT: B  566 ASP cc_start: 0.7721 (t70) cc_final: 0.7462 (t70)
REVERT: D  599 PHE cc_start: 0.8792 (t80) cc_final: 0.8465 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0876
  time to fit residues: 10.7020
Evaluate side-chains
  63 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 165 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.128323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.085611 restraints weight = 21999.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.085920 restraints weight = 16476.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.085995 restraints weight = 13941.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.086733 restraints weight = 12430.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.086908 restraints weight = 11006.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8086  Z= 0.121
  Angle     :  0.663   9.114  11025  Z= 0.337
  Chirality :  0.045   0.214   1254
  Planarity :  0.005   0.050   1419
  Dihedral  :  5.267  25.200   1074
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.38 (0.26), residues: 1001
  helix:  0.63 (0.38), residues: 180
  sheet: -1.28 (0.35), residues: 236
  loop : -2.56 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 124 
 TYR   0.012   0.001   TYR C 133 
 PHE   0.021   0.001   PHE B 594 
 TRP   0.036   0.001   TRP D 584 
 HIS   0.004   0.001   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8076)
  covalent geometry    : angle       0.66239 (11005)
  SS BOND              : bond        0.00355 (   10)
  SS BOND              : angle       0.96500 (   20)
  hydrogen bonds       : bond        0.03556 (  233)
  hydrogen bonds       : angle       5.28832 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1372.27 seconds
wall clock time: 24 minutes 21.05 seconds (1461.05 seconds total)