Starting phenix.real_space_refine
on Sat Aug 23 04:48:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l9p_62912/08_2025/9l9p_62912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l9p_62912/08_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_62912/08_2025/9l9p_62912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l9p_62912/08_2025/9l9p_62912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l9p_62912/08_2025/9l9p_62912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l9p_62912/08_2025/9l9p_62912.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.87, per 1000 atoms: 0.19
  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: 0.77
  Conformation dependent library (CDL) restraints added in 267.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.40
  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: 1.44

  Time building geometry restraints manager: 0.99 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:             0.840
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     10.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.200
-------------------------------------------------------------------------------
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 : 10.15
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG S 356 
 TYR   0.011   0.001   TYR S 286 
 PHE   0.036   0.001   PHE H 113 
 TRP   0.015   0.002   TRP S 269 
 HIS   0.001   0.001   HIS J  48 

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

*********************** 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  : 0.289 
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: 0.0858
  time to fit residues: 21.3965
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  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0170
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    4.8026

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.074986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.064702 restraints weight = 46748.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.066182 restraints weight = 24674.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.067176 restraints weight = 15387.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.067866 restraints weight = 10772.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068345 restraints weight = 8186.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10222  Z= 0.235
  Angle     :  0.944  42.139  13869  Z= 0.407
  Chirality :  0.051   0.217   1503
  Planarity :  0.005   0.070   1820
  Dihedral  :  5.794  28.004   1391
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 11.63 %
    Favored  : 87.58 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.20 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.23), residues: 1264
  helix:  0.46 (0.40), residues: 168
  sheet: -0.01 (0.30), residues: 321
  loop : -2.62 (0.20), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG S 697 
 TYR   0.030   0.002   TYR J 160 
 PHE   0.029   0.002   PHE S  47 
 TRP   0.043   0.003   TRP S 490 
 HIS   0.004   0.001   HIS S 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (10220)
  covalent geometry    : angle       0.75760 (13863)
  hydrogen bonds       : bond        0.04710 (  244)
  hydrogen bonds       : angle       5.99723 (  690)
  metal coordination   : bond        0.01741 (    2)
  metal coordination   : angle      27.05006 (    6)

*********************** 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
  181 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7298 (mpp) cc_final: 0.7009 (mpp)
REVERT: S  802 ASP cc_start: 0.8458 (t0) cc_final: 0.7922 (t0)
REVERT: A  120 MET cc_start: 0.8374 (ttp) cc_final: 0.8012 (ttp)
REVERT: A  150 GLU cc_start: 0.8602 (pm20) cc_final: 0.8217 (pp20)
REVERT: J  165 VAL cc_start: 0.9006 (t) cc_final: 0.8780 (m)
REVERT: H   36 MET cc_start: 0.8426 (mtp) cc_final: 0.7610 (ptt)
REVERT: H   49 GLU cc_start: 0.9339 (tt0) cc_final: 0.9122 (tt0)
REVERT: H   89 LYS cc_start: 0.9405 (mttm) cc_final: 0.9175 (mttm)
REVERT: H  104 GLU cc_start: 0.8818 (tt0) cc_final: 0.8406 (mt-10)
REVERT: H  111 GLU cc_start: 0.8518 (tt0) cc_final: 0.8103 (tm-30)
REVERT: B  934 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8664 (tmtt)
REVERT: B  936 MET cc_start: 0.7390 (ttt) cc_final: 0.7151 (ttt)
  outliers start: 1
  outliers final: 1
  residues processed: 181
  average time/residue: 0.0809
  time to fit residues: 21.1340
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  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 18 optimal weight:   30.0000
   chunk 85 optimal weight:    3.9990
   chunk 114 optimal weight:    8.9990
   chunk 88 optimal weight:    0.2980
   chunk 46 optimal weight:    0.0670
   chunk 103 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0010
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.4324

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.078368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.068276 restraints weight = 45678.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.069742 restraints weight = 24659.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.070792 restraints weight = 15579.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.071434 restraints weight = 10912.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.071937 restraints weight = 8392.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10222  Z= 0.117
  Angle     :  0.834  40.796  13869  Z= 0.349
  Chirality :  0.048   0.156   1503
  Planarity :  0.005   0.089   1820
  Dihedral  :  5.243  28.042   1391
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.62 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.23), residues: 1264
  helix:  0.83 (0.41), residues: 167
  sheet:  0.30 (0.30), residues: 320
  loop : -2.46 (0.20), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG H  48 
 TYR   0.026   0.001   TYR J 160 
 PHE   0.011   0.001   PHE J 227 
 TRP   0.018   0.002   TRP S 745 
 HIS   0.002   0.001   HIS S 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10220)
  covalent geometry    : angle       0.66903 (13863)
  hydrogen bonds       : bond        0.03790 (  244)
  hydrogen bonds       : angle       5.46671 (  690)
  metal coordination   : bond        0.00860 (    2)
  metal coordination   : angle      23.94581 (    6)

*********************** 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
  176 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7306 (mpp) cc_final: 0.6951 (mpp)
REVERT: S  125 MET cc_start: 0.9160 (tpp) cc_final: 0.8623 (tpp)
REVERT: A  120 MET cc_start: 0.8440 (ttp) cc_final: 0.7847 (ttp)
REVERT: J  165 VAL cc_start: 0.8928 (t) cc_final: 0.8678 (m)
REVERT: H   36 MET cc_start: 0.8220 (mtp) cc_final: 0.7462 (ptt)
REVERT: H   89 LYS cc_start: 0.9333 (mttm) cc_final: 0.8991 (mttm)
REVERT: H  104 GLU cc_start: 0.8829 (tt0) cc_final: 0.8360 (mt-10)
REVERT: H  111 GLU cc_start: 0.8796 (tt0) cc_final: 0.7857 (tm-30)
REVERT: B  931 MET cc_start: 0.9107 (mmp) cc_final: 0.8363 (ttt)
REVERT: B  934 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8655 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0904
  time to fit residues: 21.9197
Evaluate side-chains
  129 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 88 optimal weight:    9.9990
   chunk 111 optimal weight:    0.4980
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 75 optimal weight:    0.0020
   chunk 65 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.6190

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.079078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.068691 restraints weight = 45446.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.070225 restraints weight = 24487.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.071281 restraints weight = 15449.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.071980 restraints weight = 10903.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.072477 restraints weight = 8333.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10222  Z= 0.109
  Angle     :  0.763  33.030  13869  Z= 0.329
  Chirality :  0.047   0.165   1503
  Planarity :  0.004   0.055   1820
  Dihedral  :  4.984  28.295   1391
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  9.34 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.23), residues: 1264
  helix:  0.91 (0.42), residues: 167
  sheet:  0.52 (0.31), residues: 302
  loop : -2.30 (0.20), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S 127 
 TYR   0.020   0.001   TYR S 286 
 PHE   0.010   0.001   PHE J  40 
 TRP   0.017   0.001   TRP S 745 
 HIS   0.001   0.000   HIS J  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10220)
  covalent geometry    : angle       0.63653 (13863)
  hydrogen bonds       : bond        0.03264 (  244)
  hydrogen bonds       : angle       5.19183 (  690)
  metal coordination   : bond        0.01002 (    2)
  metal coordination   : angle      20.21000 (    6)

*********************** 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
  171 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7341 (mpp) cc_final: 0.6979 (mpp)
REVERT: S  535 LYS cc_start: 0.9085 (pttm) cc_final: 0.8654 (ptpp)
REVERT: S  644 MET cc_start: 0.3754 (mtt) cc_final: 0.3187 (mtt)
REVERT: A  120 MET cc_start: 0.8392 (ttp) cc_final: 0.7811 (ttp)
REVERT: A  150 GLU cc_start: 0.7753 (pp20) cc_final: 0.7363 (pp20)
REVERT: A  152 GLN cc_start: 0.7327 (mm-40) cc_final: 0.7067 (mm-40)
REVERT: H   36 MET cc_start: 0.8408 (mtp) cc_final: 0.7537 (ptt)
REVERT: H   49 GLU cc_start: 0.8972 (tt0) cc_final: 0.8363 (tt0)
REVERT: H   89 LYS cc_start: 0.9491 (mtpp) cc_final: 0.9289 (mttm)
REVERT: H   91 ASN cc_start: 0.9076 (p0) cc_final: 0.8160 (m110)
REVERT: H  104 GLU cc_start: 0.8665 (tt0) cc_final: 0.8418 (mt-10)
REVERT: H  111 GLU cc_start: 0.8598 (tt0) cc_final: 0.7966 (tm-30)
REVERT: B  931 MET cc_start: 0.9104 (mmp) cc_final: 0.8324 (ttt)
REVERT: B  934 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8629 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0753
  time to fit residues: 18.6284
Evaluate side-chains
  133 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0570
   chunk 27 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 112 optimal weight:   20.0000
   chunk 32 optimal weight:    0.6980
   chunk 109 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0070
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.9520

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.077985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.067710 restraints weight = 45625.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.069183 restraints weight = 24725.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.070193 restraints weight = 15709.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.070862 restraints weight = 11043.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.071343 restraints weight = 8487.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10222  Z= 0.122
  Angle     :  0.759  31.393  13869  Z= 0.333
  Chirality :  0.047   0.165   1503
  Planarity :  0.004   0.054   1820
  Dihedral  :  4.963  28.125   1391
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  9.57 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.24), residues: 1264
  helix:  1.04 (0.42), residues: 165
  sheet:  0.39 (0.30), residues: 309
  loop : -2.23 (0.21), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S 697 
 TYR   0.021   0.001   TYR S 286 
 PHE   0.021   0.001   PHE S  47 
 TRP   0.022   0.002   TRP J 197 
 HIS   0.002   0.000   HIS J  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10220)
  covalent geometry    : angle       0.64131 (13863)
  hydrogen bonds       : bond        0.03422 (  244)
  hydrogen bonds       : angle       5.06124 (  690)
  metal coordination   : bond        0.00475 (    2)
  metal coordination   : angle      19.50961 (    6)

*********************** 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
  159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   53 MET cc_start: 0.7696 (mtp) cc_final: 0.7265 (mtp)
REVERT: S   88 MET cc_start: 0.7405 (mpp) cc_final: 0.7057 (mpp)
REVERT: S  644 MET cc_start: 0.3972 (mtt) cc_final: 0.3399 (mtt)
REVERT: S  788 MET cc_start: 0.8356 (mmm) cc_final: 0.7669 (mpp)
REVERT: A  120 MET cc_start: 0.8232 (ttp) cc_final: 0.7769 (ttp)
REVERT: H   36 MET cc_start: 0.8308 (mtp) cc_final: 0.7519 (ptt)
REVERT: H   49 GLU cc_start: 0.8968 (tt0) cc_final: 0.8341 (tt0)
REVERT: H  104 GLU cc_start: 0.8672 (tt0) cc_final: 0.8229 (mt-10)
REVERT: H  111 GLU cc_start: 0.8553 (tt0) cc_final: 0.8022 (tm-30)
REVERT: B  934 LYS cc_start: 0.9237 (ttmm) cc_final: 0.8736 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0760
  time to fit residues: 17.7702
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  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3340 r_free = 0.3340 target = 0.081610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.073211 restraints weight = 55208.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.074334 restraints weight = 31215.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.075089 restraints weight = 20149.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.075537 restraints weight = 14425.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.075933 restraints weight = 11427.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10222  Z= 0.177
  Angle     :  0.810  31.899  13869  Z= 0.359
  Chirality :  0.048   0.165   1503
  Planarity :  0.004   0.054   1820
  Dihedral  :  5.299  31.901   1391
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 11.23 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.23), residues: 1264
  helix:  1.17 (0.42), residues: 159
  sheet:  0.17 (0.30), residues: 317
  loop : -2.36 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S 501 
 TYR   0.021   0.002   TYR S 286 
 PHE   0.028   0.002   PHE S  47 
 TRP   0.017   0.002   TRP H  76 
 HIS   0.003   0.001   HIS J  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10220)
  covalent geometry    : angle       0.68469 (13863)
  hydrogen bonds       : bond        0.03751 (  244)
  hydrogen bonds       : angle       5.18824 (  690)
  metal coordination   : bond        0.00723 (    2)
  metal coordination   : angle      20.79089 (    6)

*********************** 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
  154 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.263 
Fit side-chains
REVERT: S   53 MET cc_start: 0.7903 (mtp) cc_final: 0.7321 (mtp)
REVERT: S   88 MET cc_start: 0.7570 (mpp) cc_final: 0.7217 (mpp)
REVERT: S  125 MET cc_start: 0.8929 (ttp) cc_final: 0.8200 (tmm)
REVERT: S  496 MET cc_start: 0.8848 (pmm) cc_final: 0.8415 (pmm)
REVERT: S  644 MET cc_start: 0.3765 (mtt) cc_final: 0.3203 (mtt)
REVERT: S  788 MET cc_start: 0.8510 (mmm) cc_final: 0.7792 (mpp)
REVERT: S  802 ASP cc_start: 0.8464 (t0) cc_final: 0.7793 (t0)
REVERT: A  120 MET cc_start: 0.8368 (ttp) cc_final: 0.7903 (ttp)
REVERT: J   60 MET cc_start: 0.9086 (mtp) cc_final: 0.8884 (mtm)
REVERT: J  115 MET cc_start: 0.8771 (mtm) cc_final: 0.8555 (mtm)
REVERT: H   36 MET cc_start: 0.8372 (mtp) cc_final: 0.7463 (ptt)
REVERT: H  104 GLU cc_start: 0.8676 (tt0) cc_final: 0.8261 (mt-10)
REVERT: H  111 GLU cc_start: 0.8472 (tt0) cc_final: 0.7978 (tm-30)
REVERT: B  931 MET cc_start: 0.9172 (mmp) cc_final: 0.8354 (mtp)
REVERT: B  934 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8784 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0686
  time to fit residues: 15.7163
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  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 112 optimal weight:   30.0000
   chunk 58 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3217 r_free = 0.3217 target = 0.074025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.064077 restraints weight = 47303.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.065408 restraints weight = 26407.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.066311 restraints weight = 17100.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.066925 restraints weight = 12255.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.067312 restraints weight = 9540.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3474

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= 0.195
  Angle     :  0.796  25.230  13869  Z= 0.371
  Chirality :  0.048   0.173   1503
  Planarity :  0.005   0.055   1820
  Dihedral  :  5.510  30.726   1391
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 10.92 %
    Favored  : 88.29 %
  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 : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.23), residues: 1264
  helix:  1.23 (0.42), residues: 153
  sheet: -0.09 (0.29), residues: 328
  loop : -2.42 (0.21), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG S 697 
 TYR   0.018   0.002   TYR S 286 
 PHE   0.027   0.002   PHE S  47 
 TRP   0.027   0.002   TRP S 490 
 HIS   0.003   0.001   HIS J  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (10220)
  covalent geometry    : angle       0.70715 (13863)
  hydrogen bonds       : bond        0.03885 (  244)
  hydrogen bonds       : angle       5.24127 (  690)
  metal coordination   : bond        0.00804 (    2)
  metal coordination   : angle      17.58749 (    6)

*********************** 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
  149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: S   53 MET cc_start: 0.7616 (mtp) cc_final: 0.7157 (mtp)
REVERT: S   88 MET cc_start: 0.7704 (mpp) cc_final: 0.7294 (mpp)
REVERT: S  125 MET cc_start: 0.8989 (ttp) cc_final: 0.8225 (tmm)
REVERT: S  320 MET cc_start: 0.9313 (mmm) cc_final: 0.9106 (mmm)
REVERT: S  496 MET cc_start: 0.8911 (pmm) cc_final: 0.8578 (pmm)
REVERT: S  644 MET cc_start: 0.3883 (mtt) cc_final: 0.3335 (mtt)
REVERT: S  788 MET cc_start: 0.8529 (mmm) cc_final: 0.7792 (mpp)
REVERT: S  802 ASP cc_start: 0.8582 (t0) cc_final: 0.8016 (t0)
REVERT: A  120 MET cc_start: 0.8381 (ttp) cc_final: 0.7939 (ttp)
REVERT: J   60 MET cc_start: 0.9135 (mtp) cc_final: 0.8893 (mtm)
REVERT: J  115 MET cc_start: 0.8642 (mtm) cc_final: 0.8367 (mtm)
REVERT: H   36 MET cc_start: 0.8368 (mtp) cc_final: 0.7454 (ptt)
REVERT: H  110 MET cc_start: 0.8893 (mtp) cc_final: 0.8662 (mtt)
REVERT: B  931 MET cc_start: 0.9155 (mmp) cc_final: 0.8442 (ttt)
REVERT: B  934 LYS cc_start: 0.9298 (ttmm) cc_final: 0.8837 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0730
  time to fit residues: 15.8034
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  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 58 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 118 optimal weight:    4.9990
   overall best weight:    4.9990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.073071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.063187 restraints weight = 47740.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.064549 restraints weight = 25973.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.065466 restraints weight = 16515.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.066044 restraints weight = 11683.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.066493 restraints weight = 9083.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10222  Z= 0.219
  Angle     :  0.805  26.321  13869  Z= 0.387
  Chirality :  0.049   0.177   1503
  Planarity :  0.005   0.061   1820
  Dihedral  :  5.784  38.541   1391
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 12.58 %
    Favored  : 86.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.23), residues: 1264
  helix:  1.24 (0.42), residues: 153
  sheet: -0.15 (0.29), residues: 330
  loop : -2.46 (0.21), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG S 697 
 TYR   0.020   0.002   TYR S 286 
 PHE   0.034   0.002   PHE S  47 
 TRP   0.035   0.003   TRP S 490 
 HIS   0.003   0.001   HIS J  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (10220)
  covalent geometry    : angle       0.73534 (13863)
  hydrogen bonds       : bond        0.04093 (  244)
  hydrogen bonds       : angle       5.32487 (  690)
  metal coordination   : bond        0.00934 (    2)
  metal coordination   : angle      15.79083 (    6)

*********************** 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
  148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7809 (mpp) cc_final: 0.7414 (mpp)
REVERT: S  496 MET cc_start: 0.8919 (pmm) cc_final: 0.8559 (pmm)
REVERT: S  582 ASP cc_start: 0.8592 (t70) cc_final: 0.8370 (t70)
REVERT: S  644 MET cc_start: 0.3925 (mtt) cc_final: 0.3370 (mtt)
REVERT: S  674 GLN cc_start: 0.8833 (pt0) cc_final: 0.8584 (tm-30)
REVERT: S  788 MET cc_start: 0.8644 (mmm) cc_final: 0.7776 (mpp)
REVERT: A  120 MET cc_start: 0.8411 (ttp) cc_final: 0.7958 (ttp)
REVERT: J   60 MET cc_start: 0.9182 (mtp) cc_final: 0.8905 (mtm)
REVERT: H   36 MET cc_start: 0.8452 (mtp) cc_final: 0.7543 (ptt)
REVERT: H   89 LYS cc_start: 0.9256 (mttp) cc_final: 0.8982 (mmtp)
REVERT: H  110 MET cc_start: 0.8925 (mtp) cc_final: 0.8290 (mtp)
REVERT: B  931 MET cc_start: 0.9169 (mmp) cc_final: 0.8429 (ttt)
REVERT: B  934 LYS cc_start: 0.9312 (ttmm) cc_final: 0.8853 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0751
  time to fit residues: 16.1327
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  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 67 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0770
   overall best weight:    2.7344

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.074809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.065017 restraints weight = 46914.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.066322 restraints weight = 26473.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067226 restraints weight = 17209.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.067847 restraints weight = 12332.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.068234 restraints weight = 9554.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3805

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= 0.146
  Angle     :  0.731  23.197  13869  Z= 0.355
  Chirality :  0.048   0.169   1503
  Planarity :  0.004   0.055   1820
  Dihedral  :  5.502  34.677   1391
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.08 %
    Favored  : 88.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.23), residues: 1264
  helix:  1.12 (0.42), residues: 159
  sheet: -0.16 (0.28), residues: 344
  loop : -2.49 (0.21), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S 430 
 TYR   0.022   0.001   TYR S 211 
 PHE   0.025   0.001   PHE S  47 
 TRP   0.025   0.002   TRP S 490 
 HIS   0.003   0.001   HIS J  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10220)
  covalent geometry    : angle       0.68412 (13863)
  hydrogen bonds       : bond        0.03601 (  244)
  hydrogen bonds       : angle       5.14432 (  690)
  metal coordination   : bond        0.02114 (    2)
  metal coordination   : angle      12.33816 (    6)

*********************** 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
  148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.388 
Fit side-chains
REVERT: S   88 MET cc_start: 0.7809 (mpp) cc_final: 0.7400 (mpp)
REVERT: S  496 MET cc_start: 0.8787 (pmm) cc_final: 0.8555 (pmm)
REVERT: S  580 LYS cc_start: 0.5959 (mmpt) cc_final: 0.5122 (mmmt)
REVERT: S  644 MET cc_start: 0.3928 (mtt) cc_final: 0.3344 (mtt)
REVERT: S  788 MET cc_start: 0.8498 (mmm) cc_final: 0.7717 (mpp)
REVERT: A  120 MET cc_start: 0.8533 (ttp) cc_final: 0.8064 (ttp)
REVERT: J   60 MET cc_start: 0.9199 (mtp) cc_final: 0.8963 (mtm)
REVERT: H   36 MET cc_start: 0.8395 (mtp) cc_final: 0.7454 (ptt)
REVERT: B  931 MET cc_start: 0.9137 (mmp) cc_final: 0.8380 (ttt)
REVERT: B  934 LYS cc_start: 0.9281 (ttmm) cc_final: 0.8773 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0804
  time to fit residues: 17.3843
Evaluate side-chains
  127 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 86 optimal weight:    0.0270
   chunk 63 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0970
   chunk 98 optimal weight:   10.0000
   overall best weight:    3.0040

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

Flipped N/Q/H residues before XYZ refinement:
S 105 ASN
S 238 ASN
** S 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 665 GLN
A 138 GLN
J  64 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.074470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.064670 restraints weight = 47168.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.065981 restraints weight = 26330.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.066882 restraints weight = 17003.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.067496 restraints weight = 12137.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.067914 restraints weight = 9397.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10222  Z= 0.154
  Angle     :  0.722  21.661  13869  Z= 0.356
  Chirality :  0.048   0.178   1503
  Planarity :  0.004   0.054   1820
  Dihedral  :  5.481  35.535   1391
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.39 %
    Favored  : 87.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.23), residues: 1264
  helix:  1.14 (0.42), residues: 159
  sheet: -0.09 (0.29), residues: 332
  loop : -2.51 (0.21), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S 501 
 TYR   0.019   0.001   TYR S 286 
 PHE   0.026   0.002   PHE S  47 
 TRP   0.024   0.002   TRP S 490 
 HIS   0.002   0.001   HIS S 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10220)
  covalent geometry    : angle       0.68331 (13863)
  hydrogen bonds       : bond        0.03596 (  244)
  hydrogen bonds       : angle       5.11086 (  690)
  metal coordination   : bond        0.00678 (    2)
  metal coordination   : angle      11.27786 (    6)

********************** 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
  148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: S   88 MET cc_start: 0.7771 (mpp) cc_final: 0.7382 (mpp)
REVERT: S  580 LYS cc_start: 0.5756 (mmpt) cc_final: 0.5140 (mmmt)
REVERT: S  644 MET cc_start: 0.4061 (mtt) cc_final: 0.3457 (mtt)
REVERT: S  788 MET cc_start: 0.8476 (mmm) cc_final: 0.7689 (mpp)
REVERT: A  120 MET cc_start: 0.8525 (ttp) cc_final: 0.8061 (ttp)
REVERT: J   60 MET cc_start: 0.9156 (mtp) cc_final: 0.8893 (mtm)
REVERT: J  115 MET cc_start: 0.8597 (mtm) cc_final: 0.8291 (mtm)
REVERT: H   36 MET cc_start: 0.8339 (mtp) cc_final: 0.7408 (ptt)
REVERT: B  931 MET cc_start: 0.9118 (mmp) cc_final: 0.8410 (ttt)
REVERT: B  932 MET cc_start: 0.9201 (mtt) cc_final: 0.8989 (mtm)
REVERT: B  934 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8815 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0786
  time to fit residues: 16.8696
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  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 121 optimal weight:    9.9990
   chunk 70 optimal weight:    8.9990
   chunk 104 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 111 optimal weight:   30.0000
   chunk 118 optimal weight:    0.0070
   overall best weight:    3.9804

-------------------------------------------------------------------------------
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
A 138 GLN
J  64 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.075308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.066090 restraints weight = 52003.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.067259 restraints weight = 30143.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068041 restraints weight = 19924.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.068600 restraints weight = 14490.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.068894 restraints weight = 11413.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10222  Z= 0.183
  Angle     :  0.744  21.806  13869  Z= 0.369
  Chirality :  0.048   0.178   1503
  Planarity :  0.005   0.055   1820
  Dihedral  :  5.574  35.598   1391
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  : 12.10 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.23), residues: 1264
  helix:  1.08 (0.42), residues: 159
  sheet: -0.09 (0.29), residues: 325
  loop : -2.47 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S 127 
 TYR   0.023   0.002   TYR S 107 
 PHE   0.028   0.002   PHE S  47 
 TRP   0.025   0.002   TRP S 490 
 HIS   0.002   0.001   HIS S 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (10220)
  covalent geometry    : angle       0.70772 (13863)
  hydrogen bonds       : bond        0.03758 (  244)
  hydrogen bonds       : angle       5.15860 (  690)
  metal coordination   : bond        0.00399 (    2)
  metal coordination   : angle      11.07586 (    6)

===============================================================================
Job complete
usr+sys time: 1312.83 seconds
wall clock time: 23 minutes 29.25 seconds (1409.25 seconds total)