Starting phenix.real_space_refine
on Sat Oct 11 12:08:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8siy_40522/10_2025/8siy_40522.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8siy_40522/10_2025/8siy_40522.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8siy_40522/10_2025/8siy_40522.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8siy_40522/10_2025/8siy_40522.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8siy_40522/10_2025/8siy_40522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8siy_40522/10_2025/8siy_40522.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.045
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
     P     294      5.49       5
     S      33      5.16       5
     C    8443      2.51       5
     N    2738      2.21       5
     O    3336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14844
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2654
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 18, 'TRANS': 322}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "D"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "E"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "F"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "G"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "H"
      Number of atoms: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 697
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ML3:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 825
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "J"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "K"
      Number of atoms: 2993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2993
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "L"
      Number of atoms: 3034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3034
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "B"
      Number of atoms: 137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 137
          Classifications: {'peptide': 18}
          Link IDs: {'PTRANS': 1, 'TRANS': 16}
  Time building chain proxies: 3.46, per 1000 atoms: 0.23
  Number of scatterers: 14844
  At special positions: 0
  Unit cell: (112.32, 114.816, 123.136, 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)
     S      33     16.00
     P     294     15.00
     O    3336      8.00
     N    2738      7.00
     C    8443      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: 0.90
  Conformation dependent library (CDL) restraints added in 404.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 18 sheets defined
      51.3% alpha, 14.2% beta
      144 base pairs and 249 stacking pairs defined.
    Time for finding SS restraints: 2.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 3.678A  pdb=" N   ASN A 284 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 533
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'C' and resid 44 through 57
    Processing helix  chain 'C' and resid 63 through 77
      removed outlier: 3.785A  pdb=" N   ASP C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 132
      removed outlier: 3.524A  pdb=" N   ILE C 124 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 29
      removed outlier: 3.612A  pdb=" N   GLN D  27 " --> pdb=" O   ASP D  24 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.613A  pdb=" N   GLU D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 93
    Processing helix  chain 'E' and resid 16 through 22
    Processing helix  chain 'E' and resid 26 through 37
    Processing helix  chain 'E' and resid 45 through 73
      removed outlier: 4.378A  pdb=" N   VAL E  49 " --> pdb=" O   ALA E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 79 through 90
      removed outlier: 3.516A  pdb=" N   LEU E  83 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 97
    Processing helix  chain 'F' and resid 37 through 49
    Processing helix  chain 'F' and resid 55 through 84
    Processing helix  chain 'F' and resid 90 through 102
    Processing helix  chain 'F' and resid 103 through 124
    Processing helix  chain 'G' and resid 44 through 57
    Processing helix  chain 'G' and resid 63 through 77
      removed outlier: 3.927A  pdb=" N   ASP G  77 " --> pdb=" O   GLU G  73 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
    Processing helix  chain 'H' and resid 25 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 93
      removed outlier: 3.548A  pdb=" N   VAL H  86 " --> pdb=" O   THR H  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 16 through 22
    Processing helix  chain 'I' and resid 26 through 36
    Processing helix  chain 'I' and resid 46 through 72
      removed outlier: 3.544A  pdb=" N   LEU I  65 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 79 through 90
    Processing helix  chain 'I' and resid 90 through 97
    Processing helix  chain 'I' and resid 112 through 116
    Processing helix  chain 'J' and resid 37 through 49
    Processing helix  chain 'J' and resid 55 through 84
    Processing helix  chain 'J' and resid 90 through 102
    Processing helix  chain 'J' and resid 103 through 124
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 3.595A  pdb=" N   VAL B  22 " --> pdb=" O   ASP B  19 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 621 through 626
      removed outlier: 3.769A  pdb=" N   THR A 623 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   VAL A 642 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   PHE A 276 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE A 644 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 8.943A  pdb=" N   GLN B  15 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   PHE A 276 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298
      removed outlier: 3.794A  pdb=" N   ALA A 295 " --> pdb=" O   CYS A 317 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 321 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ASP A 326 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 335 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351
      removed outlier: 3.602A  pdb=" N   SER A 345 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER A 387 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   HIS A 379 " --> pdb=" O   CYS A 385 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   CYS A 385 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 400
      removed outlier: 3.882A  pdb=" N   ARG A 417 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ILE A 418 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   THR A 439 " --> pdb=" O   ILE A 418 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU A 420 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 451
      removed outlier: 6.362A  pdb=" N   GLY A 463 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU A 449 " --> pdb=" O   LEU A 461 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   LEU A 461 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE A 459 " --> pdb=" O   PRO A 451 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   CYS A 468 " --> pdb=" O   PHE A 488 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ASN A 487 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 506
      removed outlier: 6.110A  pdb=" N   ILE A 522 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLN A 547 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU A 524 " --> pdb=" O   LEU A 545 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563
      removed outlier: 3.507A  pdb=" N   LEU A 568 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 610 through 611
    Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 84
      removed outlier: 6.871A  pdb=" N   ARG C  83 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 98
      removed outlier: 6.640A  pdb=" N   THR D  96 " --> pdb=" O   THR I 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'E' and resid 42 through 43
      removed outlier: 7.261A  pdb=" N   ARG E  42 " --> pdb=" O   ILE F  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78
    Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 102
    Processing sheet with id=AB6, first strand: chain 'G' and resid 83 through 84
      removed outlier: 7.216A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'G' and resid 118 through 119
    Processing sheet with id=AB8, first strand: chain 'I' and resid 42 through 43
      removed outlier: 7.442A  pdb=" N   ARG I  42 " --> pdb=" O   ILE J  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'I' and resid 77 through 78

    501 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      371 hydrogen bonds
      742 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      249 stacking parallelities
  Total time for adding SS restraints: 3.68

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3004
        1.33 -     1.45: 4707
        1.45 -     1.57: 7384
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 15728
  Sorted by residual:
  bond pdb=" SG  ML3 H  20 "
       pdb=" CD  ML3 H  20 "
    ideal  model  delta    sigma   weight residual
    1.815  1.752  0.063 2.00e-02 2.50e+03 9.95e+00
  bond pdb=" CB  ML3 H  20 "
       pdb=" SG  ML3 H  20 "
    ideal  model  delta    sigma   weight residual
    1.817  1.761  0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" CA  PRO A 403 "
       pdb=" CB  PRO A 403 "
    ideal  model  delta    sigma   weight residual
    1.533  1.495  0.038 1.42e-02 4.96e+03 7.09e+00
  bond pdb=" C   VAL A 338 "
       pdb=" N   PRO A 339 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.031 1.20e-02 6.94e+03 6.82e+00
  bond pdb=" CA  PRO E  26 "
       pdb=" C   PRO E  26 "
    ideal  model  delta    sigma   weight residual
    1.521  1.505  0.015 9.30e-03 1.16e+04 2.71e+00
  ... (remaining 15723 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 21874
        1.78 -     3.56: 649
        3.56 -     5.33: 20
        5.33 -     7.11: 2
        7.11 -     8.89: 2
  Bond angle restraints: 22547
  Sorted by residual:
  angle pdb=" SG  ML3 H  20 "
        pdb=" CD  ML3 H  20 "
        pdb=" CE  ML3 H  20 "
      ideal   model   delta    sigma   weight residual
     115.60  106.71    8.89 3.00e+00 1.11e-01 8.78e+00
  angle pdb=" CA  ML3 H  20 "
        pdb=" CB  ML3 H  20 "
        pdb=" SG  ML3 H  20 "
      ideal   model   delta    sigma   weight residual
     114.92  106.84    8.08 3.00e+00 1.11e-01 7.26e+00
  angle pdb=" C   TYR A 414 "
        pdb=" N   ASP A 415 "
        pdb=" CA  ASP A 415 "
      ideal   model   delta    sigma   weight residual
     122.31  117.39    4.92 2.00e+00 2.50e-01 6.06e+00
  angle pdb=" C3'  DG K -70 "
        pdb=" C2'  DG K -70 "
        pdb=" C1'  DG K -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.07   -3.47 1.50e+00 4.44e-01 5.35e+00
  angle pdb=" O4'  DG L  27 "
        pdb=" C1'  DG L  27 "
        pdb=" C2'  DG L  27 "
      ideal   model   delta    sigma   weight residual
     106.40  103.19    3.21 1.50e+00 4.44e-01 4.59e+00
  ... (remaining 22542 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.08: 7142
       34.08 -    68.16: 1490
       68.16 -   102.23: 14
      102.23 -   136.31: 2
      136.31 -   170.39: 2
  Dihedral angle restraints: 8650
    sinusoidal: 5411
      harmonic: 3239
  Sorted by residual:
  dihedral pdb=" C4'  DC L -58 "
           pdb=" C3'  DC L -58 "
           pdb=" O3'  DC L -58 "
           pdb=" P    DT L -57 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   49.61  170.39     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG L  20 "
           pdb=" C3'  DG L  20 "
           pdb=" O3'  DG L  20 "
           pdb=" P    DG L  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.40  153.60     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CA  GLU A 406 "
           pdb=" C   GLU A 406 "
           pdb=" N   THR A 407 "
           pdb=" CA  THR A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.94   19.06     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 8647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1314
       0.029 -    0.059: 766
       0.059 -    0.088: 328
       0.088 -    0.118: 134
       0.118 -    0.147: 33
  Chirality restraints: 2575
  Sorted by residual:
  chirality pdb=" CA  ILE A 418 "
            pdb=" N   ILE A 418 "
            pdb=" C   ILE A 418 "
            pdb=" CB  ILE A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.42e-01
  chirality pdb=" CA  PRO E  80 "
            pdb=" N   PRO E  80 "
            pdb=" C   PRO E  80 "
            pdb=" CB  PRO E  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 2572 not shown)

  Planarity restraints: 1830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 598 "    0.067 5.00e-02 4.00e+02   1.02e-01 1.66e+01
        pdb=" N   PRO A 599 "   -0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A 599 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 599 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 450 "    0.045 5.00e-02 4.00e+02   6.93e-02 7.67e+00
        pdb=" N   PRO A 451 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 272 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO A 273 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 273 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 273 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 1827 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 61
        2.57 -     3.16: 11356
        3.16 -     3.74: 26526
        3.74 -     4.32: 37287
        4.32 -     4.90: 54158
  Nonbonded interactions: 129388
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  90 "
            pdb=" OE1 GLU F  93 "
     model   vdw
     1.993 3.040
  nonbonded pdb=" OE2 GLU A 299 "
            pdb=" ND2 ASN A 364 "
     model   vdw
     2.068 3.120
  nonbonded pdb=" OG1 THR J  90 "
            pdb=" OE1 GLU J  93 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" NE2 GLN A 292 "
            pdb=" O   ARG H  19 "
     model   vdw
     2.093 3.120
  nonbonded pdb=" OG  SER A 561 "
            pdb=" O   VAL A 624 "
     model   vdw
     2.167 3.040
  ... (remaining 129383 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 24 through 102)
}
ncs_group {
  reference = (chain 'E' and resid 11 through 117)
  selection = chain 'I'
}
ncs_group {
  reference = (chain 'F' and resid 32 through 124)
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.280
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  15728  Z= 0.264
  Angle     :  0.644   8.890  22547  Z= 0.388
  Chirality :  0.046   0.147   2575
  Planarity :  0.006   0.102   1830
  Dihedral  : 26.203 170.390   6552
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.14 %
    Favored  : 89.48 %
  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:  1.37 (0.25), residues: 1087
  helix:  2.11 (0.21), residues: 554
  sheet:  0.38 (0.48), residues: 113
  loop : -0.58 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  92 
 TYR   0.012   0.002   TYR J 121 
 PHE   0.008   0.001   PHE C  84 
 TRP   0.008   0.001   TRP A 645 
 HIS   0.011   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 (15728)
  covalent geometry    : angle       0.64432 (22547)
  hydrogen bonds       : bond        0.11521 (  872)
  hydrogen bonds       : angle       4.40506 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 271
  time to evaluate  : 0.434 
Fit side-chains
REVERT: I   73 ASN cc_start: 0.8454 (t0) cc_final: 0.8202 (t0)
  outliers start: 13
  outliers final: 3
  residues processed: 278
  average time/residue: 0.8177
  time to fit residues: 243.6572
Evaluate side-chains
  173 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
A 529 GLN
A 567 ASN
C  76 GLN
C 108 ASN
E  73 ASN
G  76 GLN
G 108 ASN
I 112 GLN
J  49 HIS
J  67 ASN
B  15 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.079725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.051125 restraints weight = 43322.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.28
r_work: 0.2657 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  15728  Z= 0.229
  Angle     :  0.626   7.756  22547  Z= 0.361
  Chirality :  0.039   0.234   2575
  Planarity :  0.005   0.060   1830
  Dihedral  : 29.890 172.960   4438
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.12 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.70 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.25), residues: 1087
  helix:  2.63 (0.21), residues: 557
  sheet:  0.48 (0.49), residues: 113
  loop : -0.53 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 381 
 TYR   0.022   0.002   TYR A 632 
 PHE   0.011   0.002   PHE B  16 
 TRP   0.015   0.002   TRP A 550 
 HIS   0.006   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 (15728)
  covalent geometry    : angle       0.62583 (22547)
  hydrogen bonds       : bond        0.04351 (  872)
  hydrogen bonds       : angle       3.46558 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 186
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8097 (t0)
REVERT: A  620 MET cc_start: 0.7879 (mtm) cc_final: 0.7608 (ttp)
REVERT: E   64 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8810 (tp30)
REVERT: E   90 ASP cc_start: 0.8617 (t0) cc_final: 0.8130 (t0)
REVERT: F   68 ASP cc_start: 0.9251 (t0) cc_final: 0.8958 (t0)
REVERT: G   59 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7026 (pp20)
REVERT: I   73 ASN cc_start: 0.9290 (t0) cc_final: 0.8517 (t0)
REVERT: I   90 ASP cc_start: 0.7896 (t0) cc_final: 0.7612 (t0)
REVERT: J   34 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8653 (ttpp)
REVERT: J   71 GLU cc_start: 0.8961 (tp30) cc_final: 0.8711 (tp30)
  outliers start: 38
  outliers final: 14
  residues processed: 207
  average time/residue: 0.7931
  time to fit residues: 176.4057
Evaluate side-chains
  185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain E residue   64 GLU
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  113 SER
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue  122 LYS
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue  101 THR
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 121 optimal weight:    7.9990
   chunk 82 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
A 622 ASN
C  68 GLN
C  76 GLN
D  25 ASN
D  27 GLN
D  93 GLN
E 104 GLN
F  47 GLN
J  47 GLN
J  49 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.081034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.052668 restraints weight = 43842.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.29
r_work: 0.2694 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15728  Z= 0.152
  Angle     :  0.569   7.874  22547  Z= 0.333
  Chirality :  0.036   0.170   2575
  Planarity :  0.004   0.047   1830
  Dihedral  : 29.806 172.821   4434
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.12 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.19 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.02 (0.26), residues: 1087
  helix:  2.79 (0.21), residues: 558
  sheet:  0.84 (0.53), residues: 105
  loop : -0.57 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 381 
 TYR   0.017   0.002   TYR A 336 
 PHE   0.016   0.001   PHE A 630 
 TRP   0.011   0.001   TRP A 471 
 HIS   0.009   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (15728)
  covalent geometry    : angle       0.56887 (22547)
  hydrogen bonds       : bond        0.03528 (  872)
  hydrogen bonds       : angle       3.23091 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.7570 (m-70) cc_final: 0.6924 (m-70)
REVERT: A  378 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8488 (tm)
REVERT: A  439 THR cc_start: 0.8258 (m) cc_final: 0.7975 (m)
REVERT: A  620 MET cc_start: 0.7992 (mtm) cc_final: 0.7725 (ttp)
REVERT: C   59 GLU cc_start: 0.8309 (pp20) cc_final: 0.7756 (pp20)
REVERT: E   36 LYS cc_start: 0.9491 (mmtp) cc_final: 0.9219 (mmpt)
REVERT: E   90 ASP cc_start: 0.8467 (t0) cc_final: 0.8092 (t0)
REVERT: E  104 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8428 (mm-40)
REVERT: F   35 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8270 (mt-10)
REVERT: F   68 ASP cc_start: 0.9239 (t0) cc_final: 0.8869 (t0)
REVERT: F  101 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9027 (mm)
REVERT: G   59 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7017 (pp20)
REVERT: I   73 ASN cc_start: 0.9285 (t0) cc_final: 0.8504 (t0)
REVERT: J   71 GLU cc_start: 0.8956 (tp30) cc_final: 0.8695 (tp30)
REVERT: J  105 GLU cc_start: 0.8650 (tp30) cc_final: 0.8184 (tp30)
REVERT: J  108 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8321 (ttpt)
  outliers start: 26
  outliers final: 13
  residues processed: 197
  average time/residue: 0.8259
  time to fit residues: 174.5441
Evaluate side-chains
  187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain C residue  115 LYS
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  113 SER
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 131 optimal weight:    6.9990
   chunk 129 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 519 GLN
A 529 GLN
A 622 ASN
C  68 GLN
C  76 GLN
I 112 GLN
J  47 GLN
J  49 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.077456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.048816 restraints weight = 43831.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 2.29
r_work: 0.2599 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  15728  Z= 0.316
  Angle     :  0.625   7.736  22547  Z= 0.361
  Chirality :  0.041   0.152   2575
  Planarity :  0.005   0.047   1830
  Dihedral  : 30.337 174.785   4434
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.39 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.55 %
    Favored  : 76.51 %
  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:  1.76 (0.25), residues: 1087
  helix:  2.60 (0.21), residues: 559
  sheet:  0.59 (0.51), residues: 105
  loop : -0.69 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  33 
 TYR   0.016   0.002   TYR A 523 
 PHE   0.014   0.002   PHE B  16 
 TRP   0.009   0.002   TRP A 471 
 HIS   0.005   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00721 (15728)
  covalent geometry    : angle       0.62477 (22547)
  hydrogen bonds       : bond        0.04799 (  872)
  hydrogen bonds       : angle       3.37494 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.7839 (m-70) cc_final: 0.7229 (m-70)
REVERT: A  336 TYR cc_start: 0.7934 (t80) cc_final: 0.7683 (t80)
REVERT: A  423 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8761 (tp)
REVERT: A  620 MET cc_start: 0.7922 (mtm) cc_final: 0.7672 (ttp)
REVERT: C   59 GLU cc_start: 0.8600 (pp20) cc_final: 0.8216 (pm20)
REVERT: E   36 LYS cc_start: 0.9486 (mmtp) cc_final: 0.9219 (mmpt)
REVERT: E   90 ASP cc_start: 0.8675 (t0) cc_final: 0.8218 (t0)
REVERT: E  104 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8517 (mm-40)
REVERT: F   35 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8330 (mt-10)
REVERT: F  101 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9006 (mm)
REVERT: G   59 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7247 (pp20)
REVERT: I   73 ASN cc_start: 0.9208 (t0) cc_final: 0.8447 (t0)
REVERT: J   34 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8850 (ttpp)
REVERT: J   35 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: J   71 GLU cc_start: 0.9027 (tp30) cc_final: 0.8754 (tp30)
REVERT: J  105 GLU cc_start: 0.9015 (tp30) cc_final: 0.8415 (tp30)
REVERT: J  108 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8309 (ttpt)
  outliers start: 37
  outliers final: 15
  residues processed: 192
  average time/residue: 0.8366
  time to fit residues: 172.3522
Evaluate side-chains
  179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain I residue  101 THR
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 116 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 128 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 105 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
C  68 GLN
C  76 GLN
** D  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.079968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.051646 restraints weight = 43842.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.29
r_work: 0.2675 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15728  Z= 0.153
  Angle     :  0.567   9.474  22547  Z= 0.327
  Chirality :  0.036   0.177   2575
  Planarity :  0.004   0.044   1830
  Dihedral  : 29.906 173.588   4434
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.39 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.79 %
    Favored  : 75.66 %
  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:  2.01 (0.26), residues: 1087
  helix:  2.81 (0.21), residues: 558
  sheet:  0.66 (0.52), residues: 105
  loop : -0.55 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  33 
 TYR   0.018   0.002   TYR F  40 
 PHE   0.010   0.001   PHE A 506 
 TRP   0.015   0.001   TRP A 471 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (15728)
  covalent geometry    : angle       0.56697 (22547)
  hydrogen bonds       : bond        0.03404 (  872)
  hydrogen bonds       : angle       3.13664 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8512 (OUTLIER)
REVERT: A  620 MET cc_start: 0.8015 (mtm) cc_final: 0.7749 (ttp)
REVERT: A  639 SER cc_start: 0.9292 (m) cc_final: 0.8942 (p)
REVERT: C   59 GLU cc_start: 0.8621 (pp20) cc_final: 0.8210 (pm20)
REVERT: E   15 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8557 (tptm)
REVERT: E   36 LYS cc_start: 0.9484 (mmtp) cc_final: 0.9227 (mmpt)
REVERT: E   90 ASP cc_start: 0.8580 (t0) cc_final: 0.8152 (t0)
REVERT: E   92 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8827 (mm-30)
REVERT: E  104 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8557 (mm-40)
REVERT: F   68 ASP cc_start: 0.9333 (t0) cc_final: 0.8960 (t0)
REVERT: F  101 LEU cc_start: 0.9298 (mm) cc_final: 0.8946 (mm)
REVERT: G   59 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7137 (pp20)
REVERT: G   97 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8736 (mp0)
REVERT: J   34 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8768 (ttpp)
REVERT: J   35 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8316 (mm-30)
REVERT: J   71 GLU cc_start: 0.8976 (tp30) cc_final: 0.8715 (tp30)
REVERT: J  105 GLU cc_start: 0.8901 (tp30) cc_final: 0.8697 (tp30)
REVERT: J  108 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8496 (ttpt)
  outliers start: 24
  outliers final: 12
  residues processed: 194
  average time/residue: 0.8386
  time to fit residues: 174.7821
Evaluate side-chains
  185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  580 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   97 GLU
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain I residue  114 VAL
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 124 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0570
   chunk 51 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 131 optimal weight:    6.9990
   chunk 114 optimal weight:    4.9990
   overall best weight:    2.1302

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
A 622 ASN
C  68 GLN
C  76 GLN
** D  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  93 GLN
J  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.078875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.050432 restraints weight = 43385.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 2.26
r_work: 0.2644 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  15728  Z= 0.203
  Angle     :  0.583   9.769  22547  Z= 0.334
  Chirality :  0.037   0.171   2575
  Planarity :  0.004   0.045   1830
  Dihedral  : 29.974 174.213   4434
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.67 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.94 %
    Favored  : 75.88 %
  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:  2.03 (0.26), residues: 1087
  helix:  2.79 (0.21), residues: 558
  sheet:  0.66 (0.51), residues: 105
  loop : -0.49 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J  86 
 TYR   0.019   0.002   TYR F  40 
 PHE   0.020   0.001   PHE B  16 
 TRP   0.017   0.001   TRP A 471 
 HIS   0.004   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (15728)
  covalent geometry    : angle       0.58344 (22547)
  hydrogen bonds       : bond        0.03795 (  872)
  hydrogen bonds       : angle       3.13874 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 167
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A  275 HIS cc_start: 0.7982 (m-70) cc_final: 0.7469 (m170)
REVERT: A  378 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (tp)
REVERT: A  476 ASP cc_start: 0.8680 (m-30) cc_final: 0.8031 (p0)
REVERT: A  620 MET cc_start: 0.7968 (mtm) cc_final: 0.7721 (ttp)
REVERT: A  639 SER cc_start: 0.9294 (m) cc_final: 0.8946 (p)
REVERT: C   59 GLU cc_start: 0.8597 (pp20) cc_final: 0.8080 (pm20)
REVERT: E   15 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8571 (tptm)
REVERT: E   36 LYS cc_start: 0.9501 (mmtp) cc_final: 0.9251 (mmpt)
REVERT: E   90 ASP cc_start: 0.8634 (t0) cc_final: 0.8199 (t0)
REVERT: E   92 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8818 (mm-30)
REVERT: E  104 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8516 (mm-40)
REVERT: F  101 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9010 (mm)
REVERT: G   59 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7293 (pp20)
REVERT: J   34 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8786 (ttpp)
REVERT: J   35 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8269 (mm-30)
REVERT: J   71 GLU cc_start: 0.8995 (tp30) cc_final: 0.8711 (tp30)
REVERT: J  105 GLU cc_start: 0.8961 (tp30) cc_final: 0.8720 (tp30)
REVERT: J  108 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8499 (ttpt)
  outliers start: 30
  outliers final: 20
  residues processed: 185
  average time/residue: 0.8068
  time to fit residues: 160.6802
Evaluate side-chains
  188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  113 SER
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain I residue  101 THR
Chi-restraints excluded: chain I residue  114 VAL
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 529 GLN
A 622 ASN
C  76 GLN
** D  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  31 HIS
J  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.077780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.049292 restraints weight = 43562.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 2.28
r_work: 0.2611 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080  15728  Z= 0.272
  Angle     :  0.606  10.153  22547  Z= 0.347
  Chirality :  0.039   0.167   2575
  Planarity :  0.004   0.044   1830
  Dihedral  : 30.070 174.843   4434
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.76 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.68 %
    Favored  : 74.81 %
  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:  1.90 (0.26), residues: 1087
  helix:  2.71 (0.21), residues: 558
  sheet:  0.53 (0.51), residues: 106
  loop : -0.58 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J  86 
 TYR   0.022   0.002   TYR F  40 
 PHE   0.015   0.001   PHE B  16 
 TRP   0.019   0.002   TRP A 471 
 HIS   0.004   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 (15728)
  covalent geometry    : angle       0.60574 (22547)
  hydrogen bonds       : bond        0.04127 (  872)
  hydrogen bonds       : angle       3.14950 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  275 HIS cc_start: 0.8044 (m-70) cc_final: 0.7510 (m170)
REVERT: A  378 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8475 (tp)
REVERT: A  476 ASP cc_start: 0.8758 (m-30) cc_final: 0.8120 (p0)
REVERT: A  620 MET cc_start: 0.7920 (mtm) cc_final: 0.7663 (ttp)
REVERT: A  639 SER cc_start: 0.9302 (m) cc_final: 0.8963 (p)
REVERT: C   59 GLU cc_start: 0.8615 (pp20) cc_final: 0.8086 (pm20)
REVERT: E   15 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8583 (tptm)
REVERT: E   36 LYS cc_start: 0.9504 (mmtp) cc_final: 0.9249 (mmpt)
REVERT: E   90 ASP cc_start: 0.8673 (t0) cc_final: 0.8221 (t0)
REVERT: F   71 GLU cc_start: 0.8687 (tp30) cc_final: 0.8475 (tp30)
REVERT: F  101 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8996 (mm)
REVERT: G   59 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7385 (pp20)
REVERT: J   34 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8827 (ttpp)
REVERT: J   35 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8254 (mm-30)
REVERT: J   71 GLU cc_start: 0.9036 (tp30) cc_final: 0.8781 (tp30)
REVERT: J  108 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8545 (tttt)
  outliers start: 33
  outliers final: 25
  residues processed: 183
  average time/residue: 0.8131
  time to fit residues: 160.0285
Evaluate side-chains
  186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  113 SER
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain I residue  101 THR
Chi-restraints excluded: chain I residue  114 VAL
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 132 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
C  68 GLN
C  76 GLN
** D  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 104 GLN
J  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.079200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.050895 restraints weight = 43603.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 2.25
r_work: 0.2658 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15728  Z= 0.151
  Angle     :  0.578  10.533  22547  Z= 0.331
  Chirality :  0.036   0.159   2575
  Planarity :  0.004   0.044   1830
  Dihedral  : 29.977 174.100   4434
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.67 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.53 %
    Favored  : 74.39 %
  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:  2.04 (0.26), residues: 1087
  helix:  2.82 (0.21), residues: 557
  sheet:  0.51 (0.49), residues: 112
  loop : -0.47 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J  86 
 TYR   0.024   0.002   TYR F  40 
 PHE   0.016   0.001   PHE B  16 
 TRP   0.029   0.002   TRP A 471 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (15728)
  covalent geometry    : angle       0.57771 (22547)
  hydrogen bonds       : bond        0.03425 (  872)
  hydrogen bonds       : angle       3.05210 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  275 HIS cc_start: 0.8009 (m-70) cc_final: 0.7497 (m170)
REVERT: A  378 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8475 (tp)
REVERT: A  476 ASP cc_start: 0.8744 (m-30) cc_final: 0.8107 (p0)
REVERT: A  620 MET cc_start: 0.7889 (mtm) cc_final: 0.7635 (ttp)
REVERT: A  639 SER cc_start: 0.9286 (m) cc_final: 0.8936 (p)
REVERT: C   59 GLU cc_start: 0.8575 (pp20) cc_final: 0.8085 (pm20)
REVERT: E   36 LYS cc_start: 0.9495 (mmtp) cc_final: 0.9246 (mmpt)
REVERT: E   90 ASP cc_start: 0.8632 (t0) cc_final: 0.8187 (t0)
REVERT: F  101 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9033 (mm)
REVERT: G   59 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7338 (pp20)
REVERT: J   34 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8793 (ttpp)
REVERT: J   35 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8329 (mm-30)
REVERT: J   71 GLU cc_start: 0.9016 (tp30) cc_final: 0.8762 (tp30)
REVERT: J  105 GLU cc_start: 0.8827 (tp30) cc_final: 0.8616 (tp30)
REVERT: J  108 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8471 (tttt)
  outliers start: 29
  outliers final: 20
  residues processed: 183
  average time/residue: 0.7633
  time to fit residues: 150.5219
Evaluate side-chains
  183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue  115 LYS
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain I residue  114 VAL
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0670
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 127 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 117 optimal weight:    8.9990
   chunk 111 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    3.4126

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
C  68 GLN
C  76 GLN
** D  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.077334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.048796 restraints weight = 44213.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 2.29
r_work: 0.2599 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  15728  Z= 0.276
  Angle     :  0.617  12.434  22547  Z= 0.351
  Chirality :  0.039   0.164   2575
  Planarity :  0.004   0.044   1830
  Dihedral  : 30.126 175.048   4434
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.85 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.85 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.89 (0.26), residues: 1087
  helix:  2.71 (0.22), residues: 557
  sheet:  0.50 (0.50), residues: 112
  loop : -0.58 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J  86 
 TYR   0.026   0.002   TYR F  40 
 PHE   0.011   0.001   PHE B  16 
 TRP   0.026   0.002   TRP A 471 
 HIS   0.004   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 (15728)
  covalent geometry    : angle       0.61665 (22547)
  hydrogen bonds       : bond        0.04278 (  872)
  hydrogen bonds       : angle       3.16298 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  275 HIS cc_start: 0.8086 (m-70) cc_final: 0.7528 (m170)
REVERT: A  378 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8467 (tp)
REVERT: A  620 MET cc_start: 0.7854 (mtm) cc_final: 0.7595 (ttp)
REVERT: A  639 SER cc_start: 0.9304 (m) cc_final: 0.8962 (p)
REVERT: C   59 GLU cc_start: 0.8633 (pp20) cc_final: 0.8071 (pm20)
REVERT: D   92 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8599 (ttp80)
REVERT: E   13 LYS cc_start: 0.8424 (tptp) cc_final: 0.8134 (tptt)
REVERT: E   36 LYS cc_start: 0.9502 (mmtp) cc_final: 0.9245 (mmpt)
REVERT: E   90 ASP cc_start: 0.8697 (t0) cc_final: 0.8244 (t0)
REVERT: F  101 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8997 (mm)
REVERT: G   59 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7423 (pp20)
REVERT: J   34 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8845 (ttpp)
REVERT: J   35 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8296 (mm-30)
REVERT: J   71 GLU cc_start: 0.9048 (tp30) cc_final: 0.8797 (tp30)
  outliers start: 29
  outliers final: 20
  residues processed: 177
  average time/residue: 0.7524
  time to fit residues: 143.2143
Evaluate side-chains
  185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 123 optimal weight:    4.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
C  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.078293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.049959 restraints weight = 43449.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 2.24
r_work: 0.2632 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  15728  Z= 0.177
  Angle     :  0.598  12.769  22547  Z= 0.339
  Chirality :  0.037   0.185   2575
  Planarity :  0.004   0.043   1830
  Dihedral  : 30.110 174.789   4434
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.58 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 23.59 %
    Favored  : 73.96 %
  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:  1.89 (0.26), residues: 1087
  helix:  2.66 (0.21), residues: 557
  sheet:  0.55 (0.50), residues: 112
  loop : -0.53 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  86 
 TYR   0.031   0.002   TYR F  40 
 PHE   0.013   0.001   PHE B  16 
 TRP   0.030   0.002   TRP A 471 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (15728)
  covalent geometry    : angle       0.59760 (22547)
  hydrogen bonds       : bond        0.03762 (  872)
  hydrogen bonds       : angle       3.09988 ( 2185)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  275 HIS cc_start: 0.8067 (m-70) cc_final: 0.7502 (m170)
REVERT: A  378 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8486 (tp)
REVERT: A  620 MET cc_start: 0.7777 (mtm) cc_final: 0.7508 (ttp)
REVERT: A  639 SER cc_start: 0.9301 (m) cc_final: 0.8963 (p)
REVERT: C   59 GLU cc_start: 0.8627 (pp20) cc_final: 0.8076 (pm20)
REVERT: D   92 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8601 (ttp80)
REVERT: E   13 LYS cc_start: 0.8440 (tptp) cc_final: 0.8146 (tptt)
REVERT: E   36 LYS cc_start: 0.9497 (mmtp) cc_final: 0.9244 (mmpt)
REVERT: E   90 ASP cc_start: 0.8676 (t0) cc_final: 0.8246 (t0)
REVERT: E  104 GLN cc_start: 0.8824 (mm110) cc_final: 0.8613 (mm-40)
REVERT: F   71 GLU cc_start: 0.8744 (tp30) cc_final: 0.8521 (tp30)
REVERT: F  101 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9028 (mm)
REVERT: G   59 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7395 (pp20)
REVERT: J   34 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8828 (ttpp)
REVERT: J   35 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: J   71 GLU cc_start: 0.8999 (tp30) cc_final: 0.8741 (tp30)
  outliers start: 23
  outliers final: 18
  residues processed: 178
  average time/residue: 0.7879
  time to fit residues: 150.8817
Evaluate side-chains
  186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue  115 LYS
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   59 GLU
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   18 HIS
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 125 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
C  76 GLN
E 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.077557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.049182 restraints weight = 43506.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 2.24
r_work: 0.2609 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  15728  Z= 0.246
  Angle     :  0.606  12.464  22547  Z= 0.346
  Chirality :  0.038   0.162   2575
  Planarity :  0.004   0.044   1830
  Dihedral  : 30.052 175.072   4434
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.13 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.59 %
    Favored  : 73.86 %
  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:  1.88 (0.26), residues: 1087
  helix:  2.70 (0.21), residues: 557
  sheet:  0.46 (0.50), residues: 111
  loop : -0.57 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  86 
 TYR   0.029   0.002   TYR F  40 
 PHE   0.033   0.002   PHE B  16 
 TRP   0.027   0.002   TRP A 471 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (15728)
  covalent geometry    : angle       0.60628 (22547)
  hydrogen bonds       : bond        0.04061 (  872)
  hydrogen bonds       : angle       3.12741 ( 2185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4962.37 seconds
wall clock time: 85 minutes 15.87 seconds (5115.87 seconds total)