Starting phenix.real_space_refine
on Wed Apr 30 18:35:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l9p_62912/04_2025/9l9p_62912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l9p_62912/04_2025/9l9p_62912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l9p_62912/04_2025/9l9p_62912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l9p_62912/04_2025/9l9p_62912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l9p_62912/04_2025/9l9p_62912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l9p_62912/04_2025/9l9p_62912.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.002 sd=   0.819
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: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      58      5.16       5
     C    6297      2.51       5
     N    1701      2.21       5
     O    1939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9999
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "S"
      Number of atoms: 6408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 808, 6408
          Classifications: {'peptide': 808}
          Link IDs: {'PTRANS': 39, 'TRANS': 768}
    Chain: "A"
      Number of atoms: 504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 504
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "J"
      Number of atoms: 1894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1894
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 12, 'TRANS': 229}
    Chain: "H"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 902
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 5, 'TRANS': 110}
    Chain: "B"
      Number of atoms: 283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 283
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
    Chain: "J"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8290  SG  CYS J 190      28.143  46.290  97.404  1.00 30.00           S

  Time building chain proxies: 6.27, per 1000 atoms: 0.63
  Number of scatterers: 9999
  At special positions: 0
  Unit cell: (99.28, 106.08, 220.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      58     16.00
     O    1939      8.00
     N    1701      7.00
     C    6297      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.80
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 J 301 "
        pdb="FE3  SF4 J 301 " - pdb=" SG  CYS J 190 "
        pdb="FE4  SF4 J 301 " - pdb=" SG  CYS J 235 "
      Number of angles added : 6


  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2328

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 22 sheets defined
      16.9% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'S' and resid 48 through 50
      No H-bonds generated for 'chain 'S' and resid 48 through 50'
    Processing helix  chain 'S' and resid 282 through 291
      removed outlier: 3.739A  pdb=" N   TYR S 286 " --> pdb=" O   ALA S 282 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU S 288 " --> pdb=" O   VAL S 284 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 306 through 318
      removed outlier: 3.618A  pdb=" N   LEU S 310 " --> pdb=" O   ASP S 306 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP S 318 " --> pdb=" O   ALA S 314 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 343 through 353
    Processing helix  chain 'S' and resid 385 through 389
      removed outlier: 3.755A  pdb=" N   GLY S 388 " --> pdb=" O   VAL S 385 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 396 through 400
    Processing helix  chain 'S' and resid 425 through 430
      removed outlier: 3.713A  pdb=" N   ARG S 430 " --> pdb=" O   ALA S 427 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 445 through 462
      removed outlier: 3.721A  pdb=" N   ALA S 449 " --> pdb=" O   ARG S 445 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU S 461 " --> pdb=" O   LEU S 457 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ARG S 462 " --> pdb=" O   LYS S 458 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 471 through 476
      removed outlier: 3.592A  pdb=" N   GLY S 474 " --> pdb=" O   GLY S 471 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 602 through 609
      removed outlier: 3.613A  pdb=" N   GLU S 606 " --> pdb=" O   ASN S 602 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TYR S 609 " --> pdb=" O   ASP S 605 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 767 through 771
      removed outlier: 3.640A  pdb=" N   SER S 771 " --> pdb=" O   ASP S 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 108
      removed outlier: 3.893A  pdb=" N   ALA A 106 " --> pdb=" O   ILE A 102 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE A 107 " --> pdb=" O   MET A 103 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR A 108 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 4.076A  pdb=" N   LEU A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   MET A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 141
      removed outlier: 3.964A  pdb=" N   SER A 141 " --> pdb=" O   MET A 137 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 17 through 22
    Processing helix  chain 'J' and resid 55 through 66
    Processing helix  chain 'J' and resid 110 through 119
    Processing helix  chain 'J' and resid 120 through 123
      removed outlier: 4.151A  pdb=" N   MET J 123 " --> pdb=" O   ASN J 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 120 through 123'
    Processing helix  chain 'J' and resid 135 through 137
      No H-bonds generated for 'chain 'J' and resid 135 through 137'
    Processing helix  chain 'J' and resid 191 through 196
      removed outlier: 4.055A  pdb=" N   ARG J 195 " --> pdb=" O   TYR J 191 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 231 through 240
      removed outlier: 3.981A  pdb=" N   CYS J 235 " --> pdb=" O   THR J 231 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 58 through 69
      removed outlier: 3.581A  pdb=" N   VAL H  62 " --> pdb=" O   ASP H  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 922 through 942
      removed outlier: 3.611A  pdb=" N   ARG B 938 " --> pdb=" O   LYS B 934 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 945 through 955
    Processing sheet with id=AA1, first strand: chain 'S' and resid 31 through 40
      removed outlier: 3.559A  pdb=" N   PHE S 231 " --> pdb=" O   ILE S  32 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY S 225 " --> pdb=" O   VAL S  38 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LEU S 226 " --> pdb=" O   ARG S  76 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ARG S  76 " --> pdb=" O   LEU S 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 57 through 58
    Processing sheet with id=AA3, first strand: chain 'S' and resid 108 through 109
      removed outlier: 3.735A  pdb=" N   ASP S 161 " --> pdb=" O   TYR S 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 171 through 178
    Processing sheet with id=AA5, first strand: chain 'S' and resid 171 through 178
      removed outlier: 3.615A  pdb=" N   ALA S 118 " --> pdb=" O   VAL S 214 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'S' and resid 130 through 131
    Processing sheet with id=AA7, first strand: chain 'S' and resid 252 through 255
    Processing sheet with id=AA8, first strand: chain 'S' and resid 320 through 321
      removed outlier: 3.593A  pdb=" N   VAL S 321 " --> pdb=" O   GLU S 329 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU S 329 " --> pdb=" O   VAL S 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'S' and resid 358 through 360
      removed outlier: 3.873A  pdb=" N   PHE S 360 " --> pdb=" O   SER S 367 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER S 367 " --> pdb=" O   PHE S 360 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 378 through 380
      removed outlier: 6.592A  pdb=" N   TYR S 378 " --> pdb=" O   ALA S 484 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   VAL S 578 " --> pdb=" O   VAL S 597 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   VAL S 597 " --> pdb=" O   VAL S 578 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LYS S 580 " --> pdb=" O   THR S 595 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 420 through 423
      removed outlier: 3.535A  pdb=" N   GLU S 420 " --> pdb=" O   VAL S 406 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL S 406 " --> pdb=" O   GLU S 420 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   THR S 403 " --> pdb=" O   THR S 436 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   ILE S 438 " --> pdb=" O   THR S 403 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ASN S 405 " --> pdb=" O   ILE S 438 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 534 through 537
      removed outlier: 3.972A  pdb=" N   PHE S 523 " --> pdb=" O   ASP S 567 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 632 through 635
      removed outlier: 3.536A  pdb=" N   GLN S 633 " --> pdb=" O   SER S 652 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL S 641 " --> pdb=" O   MET S 644 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 632 through 635
      removed outlier: 3.536A  pdb=" N   GLN S 633 " --> pdb=" O   SER S 652 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL S 684 " --> pdb=" O   VAL S 651 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 674 through 679
      removed outlier: 4.367A  pdb=" N   VAL S 664 " --> pdb=" O   VAL S 676 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   GLN S 678 " --> pdb=" O   TYR S 662 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   TYR S 662 " --> pdb=" O   GLN S 678 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASP S 663 " --> pdb=" O   ARG S 699 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG S 667 " --> pdb=" O   GLN S 695 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLN S 695 " --> pdb=" O   ARG S 667 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY S 692 " --> pdb=" O   LEU S 718 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 730 through 734
      removed outlier: 5.018A  pdb=" N   LEU S 731 " --> pdb=" O   PHE S 747 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE S 747 " --> pdb=" O   LEU S 731 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'S' and resid 772 through 775
      removed outlier: 3.775A  pdb=" N   LEU S 772 " --> pdb=" O   SER S 762 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   GLN S 760 " --> pdb=" O   SER S 774 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG S 815 " --> pdb=" O   ARG S 797 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 42 through 47
      removed outlier: 3.819A  pdb=" N   GLY J  37 " --> pdb=" O   ALA J  42 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   VAL J  44 " --> pdb=" O   VAL J  35 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   VAL J  35 " --> pdb=" O   VAL J  44 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ARG J  46 " --> pdb=" O   ILE J  33 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ILE J  33 " --> pdb=" O   ARG J  46 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR J 132 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU J  34 " --> pdb=" O   THR J 128 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   GLU J 156 " --> pdb=" O   THR J 171 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   THR J 171 " --> pdb=" O   GLU J 156 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ASP J 169 " --> pdb=" O   PRO J 158 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'J' and resid 212 through 213
      removed outlier: 3.887A  pdb=" N   TYR J 212 " --> pdb=" O   VAL J 220 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 26 through 32
      removed outlier: 6.323A  pdb=" N   TYR H  35 " --> pdb=" O   PHE H  31 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 49 through 56
      removed outlier: 3.933A  pdb=" N   GLY H  56 " --> pdb=" O   MET H 103 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   MET H 103 " --> pdb=" O   GLY H  56 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 49 through 56
      removed outlier: 3.933A  pdb=" N   GLY H  56 " --> pdb=" O   MET H 103 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   MET H 103 " --> pdb=" O   GLY H  56 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY H  94 " --> pdb=" O   ASN H 106 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    690 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: 4.33

  Time building geometry restraints manager: 3.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 4365
        1.43 -     1.64: 5749
        1.64 -     1.85: 94
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 10220
  Sorted by residual:
  bond pdb=" CA  VAL S 386 "
       pdb=" C   VAL S 386 "
    ideal  model  delta    sigma   weight residual
    1.522  1.487  0.035 1.16e-02 7.43e+03 9.12e+00
  bond pdb=" CA  VAL S 386 "
       pdb=" CB  VAL S 386 "
    ideal  model  delta    sigma   weight residual
    1.539  1.515  0.024 1.27e-02 6.20e+03 3.69e+00
  bond pdb=" C   PHE S 390 "
       pdb=" O   PHE S 390 "
    ideal  model  delta    sigma   weight residual
    1.235  1.214  0.022 1.28e-02 6.10e+03 2.86e+00
  bond pdb=" C   GLY S 388 "
       pdb=" O   GLY S 388 "
    ideal  model  delta    sigma   weight residual
    1.235  1.212  0.023 1.35e-02 5.49e+03 2.79e+00
  bond pdb=" C   GLN S  14 "
       pdb=" N   LYS S  15 "
    ideal  model  delta    sigma   weight residual
    1.329  1.355 -0.026 1.60e-02 3.91e+03 2.74e+00
  ... (remaining 10215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 13244
        1.60 -     3.20: 495
        3.20 -     4.79: 95
        4.79 -     6.39: 24
        6.39 -     7.99: 5
  Bond angle restraints: 13863
  Sorted by residual:
  angle pdb=" N   ASP S 389 "
        pdb=" CA  ASP S 389 "
        pdb=" C   ASP S 389 "
      ideal   model   delta    sigma   weight residual
     109.06  116.79   -7.73 1.70e+00 3.46e-01 2.07e+01
  angle pdb=" C   SER S  92 "
        pdb=" CA  SER S  92 "
        pdb=" CB  SER S  92 "
      ideal   model   delta    sigma   weight residual
     116.34  110.07    6.27 1.40e+00 5.10e-01 2.01e+01
  angle pdb=" N   ARG J 236 "
        pdb=" CA  ARG J 236 "
        pdb=" C   ARG J 236 "
      ideal   model   delta    sigma   weight residual
     111.75  106.57    5.18 1.28e+00 6.10e-01 1.63e+01
  angle pdb=" C   VAL S 386 "
        pdb=" CA  VAL S 386 "
        pdb=" CB  VAL S 386 "
      ideal   model   delta    sigma   weight residual
     111.34  106.20    5.14 1.42e+00 4.96e-01 1.31e+01
  angle pdb=" N   GLU S 156 "
        pdb=" CA  GLU S 156 "
        pdb=" C   GLU S 156 "
      ideal   model   delta    sigma   weight residual
     111.02  115.06   -4.04 1.25e+00 6.40e-01 1.05e+01
  ... (remaining 13858 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 5131
       17.76 -    35.52: 729
       35.52 -    53.28: 197
       53.28 -    71.04: 21
       71.04 -    88.80: 4
  Dihedral angle restraints: 6082
    sinusoidal: 2430
      harmonic: 3652
  Sorted by residual:
  dihedral pdb=" CA  PRO S 787 "
           pdb=" C   PRO S 787 "
           pdb=" N   MET S 788 "
           pdb=" CA  MET S 788 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.57   29.43     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  VAL S 284 "
           pdb=" C   VAL S 284 "
           pdb=" N   LEU S 285 "
           pdb=" CA  LEU S 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.01   26.99     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  VAL J 189 "
           pdb=" C   VAL J 189 "
           pdb=" N   CYS J 190 "
           pdb=" CA  CYS J 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 6079 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 965
       0.036 -    0.073: 331
       0.073 -    0.109: 139
       0.109 -    0.145: 64
       0.145 -    0.182: 4
  Chirality restraints: 1503
  Sorted by residual:
  chirality pdb=" CA  VAL S 101 "
            pdb=" N   VAL S 101 "
            pdb=" C   VAL S 101 "
            pdb=" CB  VAL S 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.26e-01
  chirality pdb=" CB  ILE S 366 "
            pdb=" CA  ILE S 366 "
            pdb=" CG1 ILE S 366 "
            pdb=" CG2 ILE S 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CB  ILE S 441 "
            pdb=" CA  ILE S 441 "
            pdb=" CG1 ILE S 441 "
            pdb=" CG2 ILE S 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 1500 not shown)

  Planarity restraints: 1820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS S 528 "   -0.040 5.00e-02 4.00e+02   6.16e-02 6.07e+00
        pdb=" N   PRO S 529 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO S 529 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S 529 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 113 "   -0.012 2.00e-02 2.50e+03   1.56e-02 4.24e+00
        pdb=" CG  PHE H 113 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 113 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 113 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 113 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 113 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN S  18 "   -0.033 5.00e-02 4.00e+02   5.05e-02 4.08e+00
        pdb=" N   PRO S  19 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO S  19 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO S  19 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1817 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1262
        2.75 -     3.29: 9434
        3.29 -     3.83: 14931
        3.83 -     4.36: 15931
        4.36 -     4.90: 28532
  Nonbonded interactions: 70090
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN J 138 "
            pdb=" O   SER J 142 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" O   SER S  56 "
            pdb=" OG  SER S  56 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" NH1 ARG J  46 "
            pdb=" OE1 GLU J  78 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OG  SER S 619 "
            pdb=" OE1 GLN J 256 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" ND1 HIS J  48 "
            pdb=" O   GLY J  81 "
     model   vdw
     2.300 3.120
  ... (remaining 70085 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.960
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     31.190
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.989  10222  Z= 0.328
  Angle     :  1.112  62.997  13869  Z= 0.409
  Chirality :  0.048   0.182   1503
  Planarity :  0.004   0.062   1820
  Dihedral  : 16.915  88.800   3754
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  1.19 %
    Allowed  : 10.13 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 26.85 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.23), residues: 1264
  helix:  0.61 (0.43), residues: 158
  sheet:  0.26 (0.32), residues: 320
  loop : -2.52 (0.20), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP S 269 
 HIS   0.001   0.001   HIS J  48 
 PHE   0.036   0.001   PHE H 113 
 TYR   0.011   0.001   TYR S 286 
 ARG   0.006   0.000   ARG S 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24613 (  244)
  hydrogen bonds       : angle       8.07184 (  690)
  metal coordination   : bond        0.69920 (    2)
  metal coordination   : angle      40.21493 (    6)
  covalent geometry    : bond        0.00308 (10220)
  covalent geometry    : angle       0.73283 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 178
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.6957 (mpp) cc_final: 0.6310 (mpp)
REVERT: A  113 SER cc_start: 0.8868 (p) cc_final: 0.8586 (t)
REVERT: A  150 GLU cc_start: 0.8330 (pm20) cc_final: 0.8032 (pp20)
REVERT: J  167 ARG cc_start: 0.7142 (ttm-80) cc_final: 0.6833 (ttm170)
REVERT: H   36 MET cc_start: 0.8225 (mtm) cc_final: 0.7398 (ptt)
REVERT: H   49 GLU cc_start: 0.9040 (tt0) cc_final: 0.8368 (tt0)
REVERT: B  921 ASP cc_start: 0.6703 (t0) cc_final: 0.6500 (t0)
REVERT: B  931 MET cc_start: 0.9084 (mmp) cc_final: 0.8224 (mtp)
REVERT: B  934 LYS cc_start: 0.9282 (ttmt) cc_final: 0.8645 (tmtt)
REVERT: B  938 ARG cc_start: 0.7947 (mmt180) cc_final: 0.6875 (ttt180)
  outliers start: 4
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2491
  time to fit residues: 61.3989
Evaluate side-chains
  142 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 94 optimal weight:    0.0770
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 97 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   overall best weight:    4.6146

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

Flipped N/Q/H residues before XYZ refinement:
** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 760 GLN
J  64 GLN
J 102 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.075395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.065061 restraints weight = 46332.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.066554 restraints weight = 24489.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.067524 restraints weight = 15297.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10222  Z= 0.216
  Angle     :  0.931  41.821  13869  Z= 0.397
  Chirality :  0.050   0.205   1503
  Planarity :  0.005   0.066   1820
  Dihedral  :  5.721  27.953   1391
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 11.79 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.93 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.23), residues: 1264
  helix:  0.47 (0.40), residues: 168
  sheet:  0.03 (0.30), residues: 321
  loop : -2.61 (0.20), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP S 490 
 HIS   0.005   0.001   HIS S 785 
 PHE   0.028   0.002   PHE S  47 
 TYR   0.031   0.002   TYR J 160 
 ARG   0.012   0.001   ARG S 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04817 (  244)
  hydrogen bonds       : angle       6.03881 (  690)
  metal coordination   : bond        0.01456 (    2)
  metal coordination   : angle      26.98437 (    6)
  covalent geometry    : bond        0.00499 (10220)
  covalent geometry    : angle       0.74252 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7332 (mpp) cc_final: 0.7041 (mpp)
REVERT: A  120 MET cc_start: 0.8389 (ttp) cc_final: 0.8023 (ttp)
REVERT: A  150 GLU cc_start: 0.8605 (pm20) cc_final: 0.8210 (pp20)
REVERT: J  165 VAL cc_start: 0.8990 (t) cc_final: 0.8750 (m)
REVERT: H   36 MET cc_start: 0.8429 (mtp) cc_final: 0.7642 (ptt)
REVERT: H   49 GLU cc_start: 0.9324 (tt0) cc_final: 0.9123 (tt0)
REVERT: H   89 LYS cc_start: 0.9396 (mttm) cc_final: 0.9162 (mttm)
REVERT: H  104 GLU cc_start: 0.8809 (tt0) cc_final: 0.8415 (mt-10)
REVERT: H  111 GLU cc_start: 0.8523 (tt0) cc_final: 0.7991 (tm-30)
REVERT: B  934 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8655 (tmtt)
REVERT: B  936 MET cc_start: 0.7394 (ttt) cc_final: 0.7157 (ttt)
  outliers start: 1
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2240
  time to fit residues: 57.4118
Evaluate side-chains
  129 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0570
   chunk 80 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.9704

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

Flipped N/Q/H residues before XYZ refinement:
S 665 GLN
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.075503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.065432 restraints weight = 46685.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.066855 restraints weight = 25571.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.067802 restraints weight = 16334.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10222  Z= 0.152
  Angle     :  0.866  41.729  13869  Z= 0.360
  Chirality :  0.048   0.154   1503
  Planarity :  0.005   0.076   1820
  Dihedral  :  5.482  27.361   1391
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  9.41 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.56 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.23), residues: 1264
  helix:  1.03 (0.42), residues: 161
  sheet: -0.07 (0.30), residues: 332
  loop : -2.51 (0.20), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP S 745 
 HIS   0.002   0.001   HIS S 781 
 PHE   0.022   0.001   PHE S  47 
 TYR   0.026   0.002   TYR J 160 
 ARG   0.008   0.001   ARG S 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  244)
  hydrogen bonds       : angle       5.53549 (  690)
  metal coordination   : bond        0.00766 (    2)
  metal coordination   : angle      25.76932 (    6)
  covalent geometry    : bond        0.00352 (10220)
  covalent geometry    : angle       0.68065 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   38 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7977 (m)
REVERT: S   88 MET cc_start: 0.7509 (mpp) cc_final: 0.7174 (mpp)
REVERT: S  125 MET cc_start: 0.9228 (tpp) cc_final: 0.8634 (tpp)
REVERT: S  227 LEU cc_start: 0.7596 (tp) cc_final: 0.7359 (tp)
REVERT: A  120 MET cc_start: 0.8514 (ttp) cc_final: 0.7915 (ttp)
REVERT: J  165 VAL cc_start: 0.8945 (t) cc_final: 0.8738 (m)
REVERT: H   36 MET cc_start: 0.8345 (mtp) cc_final: 0.7502 (ptt)
REVERT: H   89 LYS cc_start: 0.9326 (mttm) cc_final: 0.9073 (mttm)
REVERT: H  104 GLU cc_start: 0.8828 (tt0) cc_final: 0.8351 (mt-10)
REVERT: H  111 GLU cc_start: 0.8820 (tt0) cc_final: 0.8315 (tm-30)
REVERT: B  931 MET cc_start: 0.9086 (mmp) cc_final: 0.8328 (ttt)
REVERT: B  934 LYS cc_start: 0.9263 (ttmm) cc_final: 0.8702 (tmtt)
REVERT: B  936 MET cc_start: 0.7430 (ttt) cc_final: 0.7185 (ttt)
  outliers start: 2
  outliers final: 1
  residues processed: 162
  average time/residue: 0.2075
  time to fit residues: 48.3229
Evaluate side-chains
  126 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 110 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 112 optimal weight:   30.0000
   chunk 34 optimal weight:    0.0980
   chunk 85 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
S  17 HIS
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.076790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.066359 restraints weight = 45388.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.067830 restraints weight = 24570.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.068864 restraints weight = 15678.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10222  Z= 0.118
  Angle     :  0.795  35.378  13869  Z= 0.339
  Chirality :  0.048   0.171   1503
  Planarity :  0.004   0.056   1820
  Dihedral  :  5.281  27.605   1391
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  9.57 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.23), residues: 1264
  helix:  0.94 (0.42), residues: 167
  sheet:  0.15 (0.30), residues: 320
  loop : -2.39 (0.21), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP S 745 
 HIS   0.002   0.001   HIS J  48 
 PHE   0.018   0.001   PHE S  47 
 TYR   0.021   0.001   TYR J 160 
 ARG   0.005   0.001   ARG S 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  244)
  hydrogen bonds       : angle       5.22993 (  690)
  metal coordination   : bond        0.00706 (    2)
  metal coordination   : angle      22.06499 (    6)
  covalent geometry    : bond        0.00273 (10220)
  covalent geometry    : angle       0.64886 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7621 (mpp) cc_final: 0.7258 (mpp)
REVERT: S  125 MET cc_start: 0.9231 (tpp) cc_final: 0.8368 (tmm)
REVERT: S  582 ASP cc_start: 0.8536 (t70) cc_final: 0.8228 (t70)
REVERT: A  120 MET cc_start: 0.8348 (ttp) cc_final: 0.7859 (ttp)
REVERT: J  115 MET cc_start: 0.8780 (mtm) cc_final: 0.8566 (mtm)
REVERT: H   36 MET cc_start: 0.8365 (mtp) cc_final: 0.7434 (ptt)
REVERT: H   49 GLU cc_start: 0.9162 (tt0) cc_final: 0.8474 (tt0)
REVERT: H   89 LYS cc_start: 0.9528 (mtpp) cc_final: 0.9033 (mttm)
REVERT: H  104 GLU cc_start: 0.8825 (tt0) cc_final: 0.8279 (mt-10)
REVERT: H  110 MET cc_start: 0.8841 (mtp) cc_final: 0.8443 (mtt)
REVERT: H  111 GLU cc_start: 0.8777 (tt0) cc_final: 0.8320 (tm-30)
REVERT: B  934 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8663 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2065
  time to fit residues: 49.7247
Evaluate side-chains
  126 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 77 optimal weight:   30.0000
   chunk 53 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 115 optimal weight:   20.0000
   chunk 81 optimal weight:    6.9990
   chunk 76 optimal weight:   30.0000
   chunk 122 optimal weight:    5.9990
   chunk 105 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 31 optimal weight:   40.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
S 239 GLN
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.073466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.063290 restraints weight = 46664.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.064682 restraints weight = 25801.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.065588 restraints weight = 16539.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10222  Z= 0.203
  Angle     :  0.793  29.630  13869  Z= 0.375
  Chirality :  0.049   0.164   1503
  Planarity :  0.005   0.056   1820
  Dihedral  :  5.607  29.002   1391
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 11.87 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.23), residues: 1264
  helix:  1.01 (0.42), residues: 159
  sheet:  0.06 (0.29), residues: 323
  loop : -2.51 (0.21), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H  76 
 HIS   0.003   0.001   HIS J  48 
 PHE   0.035   0.002   PHE S  47 
 TYR   0.021   0.002   TYR J 160 
 ARG   0.009   0.001   ARG S 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  244)
  hydrogen bonds       : angle       5.27822 (  690)
  metal coordination   : bond        0.01175 (    2)
  metal coordination   : angle      16.96594 (    6)
  covalent geometry    : bond        0.00467 (10220)
  covalent geometry    : angle       0.71044 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7682 (mpp) cc_final: 0.7286 (mpp)
REVERT: S  125 MET cc_start: 0.9020 (tpp) cc_final: 0.8351 (tpp)
REVERT: S  320 MET cc_start: 0.8969 (tpt) cc_final: 0.8729 (tpp)
REVERT: S  496 MET cc_start: 0.9042 (pmm) cc_final: 0.8550 (pmm)
REVERT: S  582 ASP cc_start: 0.8482 (t70) cc_final: 0.8253 (t70)
REVERT: S  644 MET cc_start: 0.4006 (mtt) cc_final: 0.3455 (mtt)
REVERT: A  120 MET cc_start: 0.8448 (ttp) cc_final: 0.7981 (ttp)
REVERT: J   60 MET cc_start: 0.9137 (mtp) cc_final: 0.8921 (mtm)
REVERT: J  115 MET cc_start: 0.8650 (mtm) cc_final: 0.8338 (mtm)
REVERT: H    9 TRP cc_start: 0.6922 (m-90) cc_final: 0.6495 (m-90)
REVERT: H   36 MET cc_start: 0.8377 (mtp) cc_final: 0.7483 (ptt)
REVERT: H   49 GLU cc_start: 0.9114 (tt0) cc_final: 0.8498 (tt0)
REVERT: H   89 LYS cc_start: 0.9459 (mtpp) cc_final: 0.9206 (mttm)
REVERT: H  111 GLU cc_start: 0.8768 (tt0) cc_final: 0.8400 (tm-30)
REVERT: B  931 MET cc_start: 0.9190 (mmp) cc_final: 0.8370 (mtp)
REVERT: B  934 LYS cc_start: 0.9258 (ttmm) cc_final: 0.8791 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2475
  time to fit residues: 57.3748
Evaluate side-chains
  124 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 123 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 107 optimal weight:    0.0670
   chunk 78 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 111 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    3.2126

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

Flipped N/Q/H residues before XYZ refinement:
S 238 ASN
S 239 GLN
** S 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  64 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.074309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.064062 restraints weight = 46915.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.065489 restraints weight = 25376.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.066433 restraints weight = 16089.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10222  Z= 0.162
  Angle     :  0.747  27.052  13869  Z= 0.358
  Chirality :  0.048   0.171   1503
  Planarity :  0.004   0.056   1820
  Dihedral  :  5.554  31.180   1391
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.39 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.23), residues: 1264
  helix:  1.13 (0.42), residues: 159
  sheet: -0.14 (0.29), residues: 332
  loop : -2.43 (0.21), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP S 490 
 HIS   0.003   0.001   HIS J  48 
 PHE   0.010   0.001   PHE S  75 
 TYR   0.019   0.001   TYR S 286 
 ARG   0.007   0.001   ARG S 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  244)
  hydrogen bonds       : angle       5.22221 (  690)
  metal coordination   : bond        0.00558 (    2)
  metal coordination   : angle      14.79467 (    6)
  covalent geometry    : bond        0.00379 (10220)
  covalent geometry    : angle       0.68029 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.420 
Fit side-chains
   revert: symmetry clash
REVERT: S   47 PHE cc_start: 0.6909 (m-80) cc_final: 0.6685 (m-80)
REVERT: S   53 MET cc_start: 0.7594 (mtp) cc_final: 0.7127 (mtp)
REVERT: S   88 MET cc_start: 0.7759 (mpp) cc_final: 0.7339 (mpp)
REVERT: S  496 MET cc_start: 0.8942 (pmm) cc_final: 0.8564 (pmm)
REVERT: S  582 ASP cc_start: 0.8509 (t70) cc_final: 0.8235 (t70)
REVERT: S  644 MET cc_start: 0.3889 (mtt) cc_final: 0.3313 (mtt)
REVERT: S  802 ASP cc_start: 0.8660 (t0) cc_final: 0.8281 (t0)
REVERT: A  120 MET cc_start: 0.8386 (ttp) cc_final: 0.7945 (ttp)
REVERT: J   60 MET cc_start: 0.9188 (mtp) cc_final: 0.8954 (mtm)
REVERT: J  115 MET cc_start: 0.8632 (mtm) cc_final: 0.8350 (mtm)
REVERT: H    9 TRP cc_start: 0.7010 (m-90) cc_final: 0.6408 (m-90)
REVERT: H   36 MET cc_start: 0.8432 (mtp) cc_final: 0.7487 (ptt)
REVERT: H   49 GLU cc_start: 0.9115 (tt0) cc_final: 0.8275 (tt0)
REVERT: H   89 LYS cc_start: 0.9468 (mtpp) cc_final: 0.9000 (mttm)
REVERT: H  110 MET cc_start: 0.8786 (mtp) cc_final: 0.8332 (mtt)
REVERT: H  111 GLU cc_start: 0.8802 (tt0) cc_final: 0.8365 (tm-30)
REVERT: B  931 MET cc_start: 0.9202 (mmp) cc_final: 0.8390 (ttt)
REVERT: B  934 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8766 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2367
  time to fit residues: 52.0522
Evaluate side-chains
  122 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 117 optimal weight:    8.9990
   chunk 25 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 95 optimal weight:    9.9990
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
S 239 GLN
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.073210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.063154 restraints weight = 48103.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.064520 restraints weight = 26263.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.065453 restraints weight = 16785.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10222  Z= 0.181
  Angle     :  0.756  26.109  13869  Z= 0.369
  Chirality :  0.048   0.172   1503
  Planarity :  0.005   0.057   1820
  Dihedral  :  5.650  34.993   1391
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 12.34 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.23), residues: 1264
  helix:  1.03 (0.42), residues: 159
  sheet: -0.17 (0.28), residues: 334
  loop : -2.49 (0.21), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP S 490 
 HIS   0.003   0.001   HIS J  48 
 PHE   0.016   0.002   PHE S  47 
 TYR   0.019   0.002   TYR S 211 
 ARG   0.005   0.001   ARG S 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  244)
  hydrogen bonds       : angle       5.20635 (  690)
  metal coordination   : bond        0.00494 (    2)
  metal coordination   : angle      13.56796 (    6)
  covalent geometry    : bond        0.00420 (10220)
  covalent geometry    : angle       0.70172 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
REVERT: S   53 MET cc_start: 0.7784 (mtp) cc_final: 0.7250 (mtp)
REVERT: S   88 MET cc_start: 0.7807 (mpp) cc_final: 0.7412 (mpp)
REVERT: S  125 MET cc_start: 0.9087 (tpp) cc_final: 0.8679 (tpp)
REVERT: S  496 MET cc_start: 0.8917 (pmm) cc_final: 0.8569 (pmm)
REVERT: S  644 MET cc_start: 0.4073 (mtt) cc_final: 0.3486 (mtt)
REVERT: S  788 MET cc_start: 0.8133 (mmm) cc_final: 0.7402 (mpp)
REVERT: A  120 MET cc_start: 0.8507 (ttp) cc_final: 0.8044 (ttp)
REVERT: J   60 MET cc_start: 0.9097 (mtp) cc_final: 0.8883 (mtm)
REVERT: J  115 MET cc_start: 0.8557 (mtm) cc_final: 0.8241 (mtm)
REVERT: H    9 TRP cc_start: 0.6889 (m-90) cc_final: 0.6596 (m-90)
REVERT: H   36 MET cc_start: 0.8464 (mtp) cc_final: 0.7571 (ptt)
REVERT: H  110 MET cc_start: 0.8756 (mtp) cc_final: 0.8199 (mtp)
REVERT: H  111 GLU cc_start: 0.8776 (tt0) cc_final: 0.8386 (tm-30)
REVERT: B  931 MET cc_start: 0.9191 (mmp) cc_final: 0.8447 (ttt)
REVERT: B  934 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8802 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2386
  time to fit residues: 51.5916
Evaluate side-chains
  120 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 119 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0770
   chunk 13 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   overall best weight:    2.7944

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

Flipped N/Q/H residues before XYZ refinement:
** S 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  64 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.074335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.064273 restraints weight = 47328.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.065666 restraints weight = 25782.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.066562 restraints weight = 16402.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10222  Z= 0.148
  Angle     :  0.717  20.636  13869  Z= 0.355
  Chirality :  0.048   0.168   1503
  Planarity :  0.004   0.055   1820
  Dihedral  :  5.531  36.235   1391
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.16 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.23), residues: 1264
  helix:  1.09 (0.42), residues: 159
  sheet: -0.25 (0.28), residues: 347
  loop : -2.48 (0.21), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP S 490 
 HIS   0.003   0.001   HIS J  48 
 PHE   0.024   0.001   PHE S  47 
 TYR   0.018   0.001   TYR S 286 
 ARG   0.003   0.000   ARG S 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  244)
  hydrogen bonds       : angle       5.18302 (  690)
  metal coordination   : bond        0.00917 (    2)
  metal coordination   : angle      10.58553 (    6)
  covalent geometry    : bond        0.00346 (10220)
  covalent geometry    : angle       0.68244 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
REVERT: S   53 MET cc_start: 0.7696 (mtp) cc_final: 0.7316 (mtm)
REVERT: S   88 MET cc_start: 0.7855 (mpp) cc_final: 0.7476 (mpp)
REVERT: S  125 MET cc_start: 0.9021 (tpp) cc_final: 0.8751 (tpp)
REVERT: S  496 MET cc_start: 0.8792 (pmm) cc_final: 0.8348 (pmm)
REVERT: S  580 LYS cc_start: 0.5614 (mmpt) cc_final: 0.5049 (mmmt)
REVERT: S  644 MET cc_start: 0.4184 (mtt) cc_final: 0.3561 (mtt)
REVERT: S  788 MET cc_start: 0.8084 (mmm) cc_final: 0.7373 (mpp)
REVERT: A  120 MET cc_start: 0.8562 (ttp) cc_final: 0.8109 (ttp)
REVERT: J   60 MET cc_start: 0.9156 (mtp) cc_final: 0.8933 (mtm)
REVERT: J  115 MET cc_start: 0.8556 (mtm) cc_final: 0.8253 (mtm)
REVERT: H    9 TRP cc_start: 0.6877 (m-90) cc_final: 0.6612 (m-90)
REVERT: H   36 MET cc_start: 0.8408 (mtp) cc_final: 0.7552 (ptt)
REVERT: H   89 LYS cc_start: 0.9286 (mttm) cc_final: 0.8920 (mmtp)
REVERT: H  111 GLU cc_start: 0.8647 (tt0) cc_final: 0.8294 (tm-30)
REVERT: B  931 MET cc_start: 0.9187 (mmp) cc_final: 0.8423 (ttt)
REVERT: B  934 LYS cc_start: 0.9254 (ttmm) cc_final: 0.8789 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2139
  time to fit residues: 44.7712
Evaluate side-chains
  123 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0770
   chunk 38 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0670
   overall best weight:    1.6280

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

Flipped N/Q/H residues before XYZ refinement:
** S 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 GLN
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.075359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.065141 restraints weight = 46727.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.066527 restraints weight = 25916.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.067451 restraints weight = 16716.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10222  Z= 0.121
  Angle     :  0.689  16.813  13869  Z= 0.342
  Chirality :  0.047   0.169   1503
  Planarity :  0.004   0.054   1820
  Dihedral  :  5.328  35.862   1391
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 10.68 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.23), residues: 1264
  helix:  1.19 (0.43), residues: 159
  sheet:  0.00 (0.29), residues: 319
  loop : -2.40 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  76 
 HIS   0.006   0.001   HIS J  48 
 PHE   0.017   0.001   PHE S  47 
 TYR   0.017   0.001   TYR S 286 
 ARG   0.003   0.000   ARG S 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  244)
  hydrogen bonds       : angle       5.00071 (  690)
  metal coordination   : bond        0.00417 (    2)
  metal coordination   : angle       9.06695 (    6)
  covalent geometry    : bond        0.00281 (10220)
  covalent geometry    : angle       0.66275 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7855 (mpp) cc_final: 0.7520 (mpp)
REVERT: S  125 MET cc_start: 0.9057 (tpp) cc_final: 0.8301 (tmm)
REVERT: S  496 MET cc_start: 0.8642 (pmm) cc_final: 0.8403 (pmm)
REVERT: S  580 LYS cc_start: 0.5687 (mmpt) cc_final: 0.5066 (mmmt)
REVERT: S  644 MET cc_start: 0.4173 (mtt) cc_final: 0.3585 (mtt)
REVERT: S  788 MET cc_start: 0.8431 (mmm) cc_final: 0.7711 (mpp)
REVERT: A  120 MET cc_start: 0.8525 (ttp) cc_final: 0.8072 (ttp)
REVERT: J   60 MET cc_start: 0.9195 (mtp) cc_final: 0.8972 (mtm)
REVERT: H    9 TRP cc_start: 0.6852 (m-90) cc_final: 0.6603 (m-90)
REVERT: H   36 MET cc_start: 0.8430 (mtp) cc_final: 0.7465 (ptt)
REVERT: H   89 LYS cc_start: 0.9268 (mttm) cc_final: 0.9042 (mmtt)
REVERT: H  110 MET cc_start: 0.8852 (mtp) cc_final: 0.8089 (mtp)
REVERT: H  111 GLU cc_start: 0.8579 (tt0) cc_final: 0.8222 (tm-30)
REVERT: B  931 MET cc_start: 0.9159 (mmp) cc_final: 0.8374 (ttt)
REVERT: B  934 LYS cc_start: 0.9240 (ttmm) cc_final: 0.8756 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2269
  time to fit residues: 50.0437
Evaluate side-chains
  125 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 51 optimal weight:    0.0370
   chunk 115 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 110 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0370
   chunk 18 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:   30.0000
   overall best weight:    2.1540

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

Flipped N/Q/H residues before XYZ refinement:
** S 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 GLN
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.075448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.065547 restraints weight = 47088.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.066855 restraints weight = 26752.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.067733 restraints weight = 17484.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10222  Z= 0.132
  Angle     :  0.693  16.173  13869  Z= 0.346
  Chirality :  0.048   0.187   1503
  Planarity :  0.004   0.054   1820
  Dihedral  :  5.336  35.815   1391
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.23 %
    Favored  : 88.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.23), residues: 1264
  helix:  1.14 (0.42), residues: 159
  sheet:  0.06 (0.29), residues: 318
  loop : -2.36 (0.21), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  76 
 HIS   0.002   0.001   HIS S 781 
 PHE   0.018   0.001   PHE S  47 
 TYR   0.018   0.001   TYR S 286 
 ARG   0.005   0.000   ARG S 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  244)
  hydrogen bonds       : angle       4.95746 (  690)
  metal coordination   : bond        0.00261 (    2)
  metal coordination   : angle       8.83206 (    6)
  covalent geometry    : bond        0.00309 (10220)
  covalent geometry    : angle       0.66818 (13863)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7843 (mpp) cc_final: 0.7522 (mpp)
REVERT: S  125 MET cc_start: 0.9049 (tpp) cc_final: 0.8314 (tmm)
REVERT: S  580 LYS cc_start: 0.5625 (mmpt) cc_final: 0.5009 (mmmt)
REVERT: S  644 MET cc_start: 0.4169 (mtt) cc_final: 0.3594 (mtt)
REVERT: S  788 MET cc_start: 0.8416 (mmm) cc_final: 0.7692 (mpp)
REVERT: A  120 MET cc_start: 0.8529 (ttp) cc_final: 0.8096 (ttp)
REVERT: J   60 MET cc_start: 0.9208 (mtp) cc_final: 0.8983 (mtm)
REVERT: J  176 MET cc_start: 0.8627 (mtm) cc_final: 0.7576 (ttt)
REVERT: H    9 TRP cc_start: 0.6870 (m-90) cc_final: 0.6591 (m-90)
REVERT: H   36 MET cc_start: 0.8449 (mtp) cc_final: 0.7457 (ptt)
REVERT: H  110 MET cc_start: 0.8863 (mtp) cc_final: 0.8626 (mtt)
REVERT: H  111 GLU cc_start: 0.8503 (tt0) cc_final: 0.8170 (tm-30)
REVERT: B  934 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8731 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2307
  time to fit residues: 49.5635
Evaluate side-chains
  125 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 112 optimal weight:   30.0000
   chunk 84 optimal weight:    0.0870
   chunk 60 optimal weight:    9.9990
   chunk 123 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 93 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0370
   overall best weight:    3.8242

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

Flipped N/Q/H residues before XYZ refinement:
** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 GLN
J  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.073724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.063688 restraints weight = 47675.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.065057 restraints weight = 26019.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.065948 restraints weight = 16593.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10222  Z= 0.180
  Angle     :  0.741  20.275  13869  Z= 0.369
  Chirality :  0.049   0.175   1503
  Planarity :  0.005   0.056   1820
  Dihedral  :  5.542  35.411   1391
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 12.10 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.23), residues: 1264
  helix:  1.04 (0.42), residues: 159
  sheet: -0.13 (0.28), residues: 334
  loop : -2.44 (0.21), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP S 490 
 HIS   0.002   0.001   HIS S 781 
 PHE   0.025   0.002   PHE S  47 
 TYR   0.022   0.002   TYR S 211 
 ARG   0.004   0.001   ARG S  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  244)
  hydrogen bonds       : angle       5.09856 (  690)
  metal coordination   : bond        0.00501 (    2)
  metal coordination   : angle      10.54888 (    6)
  covalent geometry    : bond        0.00421 (10220)
  covalent geometry    : angle       0.70784 (13863)

===============================================================================
Job complete
usr+sys time: 3444.87 seconds
wall clock time: 61 minutes 36.96 seconds (3696.96 seconds total)