Starting phenix.real_space_refine
on Tue Mar  3 18:07:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fbi_31515/03_2026/7fbi_31515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fbi_31515/03_2026/7fbi_31515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2026/7fbi_31515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2026/7fbi_31515.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2026/7fbi_31515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2026/7fbi_31515.map"
  }
  resolution = 3.9
  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=   0.002 sd=   0.906
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4895      2.51       5
     N    1310      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7777
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 798
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "L"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 812
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 106}
    Chain: "A"
      Number of atoms: 4467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4467
          Classifications: {'peptide': 557}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 540}
          Chain breaks: 3
    Chain: "M"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 819
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "N"
      Number of atoms: 881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 881
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
  Time building chain proxies: 1.54, per 1000 atoms: 0.20
  Number of scatterers: 7777
  At special positions: 0
  Unit cell: (69.3, 158.4, 192.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1533      8.00
     N    1310      7.00
     C    4895      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  93 " distance=2.03

  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: 0.61
  Conformation dependent library (CDL) restraints added in 223.1 milliseconds
  

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1832

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 20 sheets defined
      9.7% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.165A  pdb=" N   SER H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TYR H  32 " --> pdb=" O   LEU H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'A' and resid 128 through 132
      removed outlier: 3.720A  pdb=" N   GLU A 131 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 132 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 128 through 132'
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 3.984A  pdb=" N   ILE A 138 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 350 through 357
      removed outlier: 3.822A  pdb=" N   LYS A 354 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 467
      removed outlier: 3.919A  pdb=" N   ALA A 464 " --> pdb=" O   GLN A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 476
    Processing helix  chain 'A' and resid 480 through 497
      removed outlier: 3.633A  pdb=" N   CYS A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A 492 " --> pdb=" O   LYS A 488 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A 493 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG A 495 " --> pdb=" O   ASN A 491 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU A 496 " --> pdb=" O   MET A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 511
      removed outlier: 4.196A  pdb=" N   VAL A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   SER A 507 " --> pdb=" O   THR A 503 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   SER A 508 " --> pdb=" O   THR A 504 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A 509 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 576
      No H-bonds generated for 'chain 'A' and resid 574 through 576'
    Processing helix  chain 'A' and resid 645 through 651
      removed outlier: 3.915A  pdb=" N   ARG A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A 651 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 665
      removed outlier: 3.981A  pdb=" N   PHE A 661 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   ARG A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLU A 663 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 19 through 21
    Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59
      removed outlier: 3.530A  pdb=" N   TYR H  58 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL H  50 " --> pdb=" O   TYR H  58 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN H  39 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 23 through 24
      removed outlier: 3.592A  pdb=" N   THR L  72 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR L  74 " --> pdb=" O   ARG L  63 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 49
      removed outlier: 6.929A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 46 through 49
      removed outlier: 6.929A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLN L  38 " --> pdb=" O   THR L  85 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   THR L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 49 through 50
    Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 80
      removed outlier: 3.749A  pdb=" N   GLY A  80 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   THR A 306 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR A 311 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER A 314 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 125
      removed outlier: 3.643A  pdb=" N   ASN A 105 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE A  94 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A 213 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170
      removed outlier: 3.661A  pdb=" N   ALA A 213 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE A  94 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 277 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 145 through 149
      removed outlier: 4.072A  pdb=" N   VAL A 145 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   TYR A 156 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET A 147 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 370 through 373
      removed outlier: 3.796A  pdb=" N   THR A 370 " --> pdb=" O   TRP A 382 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TRP A 382 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE A 372 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 552
    Processing sheet with id=AB5, first strand: chain 'A' and resid 556 through 560
      removed outlier: 3.574A  pdb=" N   GLN A 571 " --> pdb=" O   PHE A 579 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 579 " --> pdb=" O   GLN A 571 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 594 through 598
      removed outlier: 3.680A  pdb=" N   TYR A 594 " --> pdb=" O   TYR A 605 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TYR A 605 " --> pdb=" O   TYR A 594 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   PHE A 596 " --> pdb=" O   HIS A 603 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   HIS A 603 " --> pdb=" O   PHE A 596 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLU A 601 " --> pdb=" O   SER A 598 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS A 612 " --> pdb=" O   VAL A 604 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 6
      removed outlier: 3.675A  pdb=" N   ILE M  21 " --> pdb=" O   LEU M  73 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   CYS M  23 " --> pdb=" O   TYR M  71 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   TYR M  71 " --> pdb=" O   CYS M  23 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP M  70 " --> pdb=" O   SER M  67 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER M  67 " --> pdb=" O   ASP M  70 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'M' and resid 35 through 38
      removed outlier: 3.744A  pdb=" N   TYR M  87 " --> pdb=" O   TYR M  36 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG M  38 " --> pdb=" O   THR M  85 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   THR M  85 " --> pdb=" O   ARG M  38 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7
      removed outlier: 3.592A  pdb=" N   THR N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL N  76 " --> pdb=" O   CYS N  22 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP N  77 " --> pdb=" O   SER N  70 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 18 through 19
      removed outlier: 3.571A  pdb=" N   MET N  80 " --> pdb=" O   LEU N  18 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'N' and resid 33 through 39
      removed outlier: 4.501A  pdb=" N   GLU N  33 " --> pdb=" O   GLY N  96 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL N  37 " --> pdb=" O   PHE N  92 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN N  39 " --> pdb=" O   THR N  90 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR N  90 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   THR N 114 " --> pdb=" O   TYR N  91 " (cutoff:3.500A)

    125 hydrogen bonds defined for protein.
    318 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1273
        1.31 -     1.44: 2253
        1.44 -     1.57: 4352
        1.57 -     1.70: 2
        1.70 -     1.83: 58
  Bond restraints: 7938
  Sorted by residual:
  bond pdb=" N   HIS A 352 "
       pdb=" CA  HIS A 352 "
    ideal  model  delta    sigma   weight residual
    1.459  1.375  0.085 1.18e-02 7.18e+03 5.16e+01
  bond pdb=" CA  ARG H  10 "
       pdb=" C   ARG H  10 "
    ideal  model  delta    sigma   weight residual
    1.523  1.598 -0.075 1.34e-02 5.57e+03 3.16e+01
  bond pdb=" C   SER M  93 "
       pdb=" O   SER M  93 "
    ideal  model  delta    sigma   weight residual
    1.235  1.178  0.057 1.26e-02 6.30e+03 2.07e+01
  bond pdb=" CA  PHE M  92 "
       pdb=" C   PHE M  92 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.050 1.12e-02 7.97e+03 2.02e+01
  bond pdb=" C   HIS A 352 "
       pdb=" N   GLU A 353 "
    ideal  model  delta    sigma   weight residual
    1.335  1.279  0.056 1.27e-02 6.20e+03 1.92e+01
  ... (remaining 7933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 10574
        3.59 -     7.18: 163
        7.18 -    10.77: 26
       10.77 -    14.36: 5
       14.36 -    17.95: 2
  Bond angle restraints: 10770
  Sorted by residual:
  angle pdb=" N   SER M  95 "
        pdb=" CA  SER M  95 "
        pdb=" C   SER M  95 "
      ideal   model   delta    sigma   weight residual
     109.24  127.19  -17.95 1.51e+00 4.39e-01 1.41e+02
  angle pdb=" C   MET A 351 "
        pdb=" N   HIS A 352 "
        pdb=" CA  HIS A 352 "
      ideal   model   delta    sigma   weight residual
     120.63  108.66   11.97 1.36e+00 5.41e-01 7.75e+01
  angle pdb=" N   GLN M  90 "
        pdb=" CA  GLN M  90 "
        pdb=" C   GLN M  90 "
      ideal   model   delta    sigma   weight residual
     112.59  122.19   -9.60 1.22e+00 6.72e-01 6.19e+01
  angle pdb=" N   GLY M  91 "
        pdb=" CA  GLY M  91 "
        pdb=" C   GLY M  91 "
      ideal   model   delta    sigma   weight residual
     111.34  125.65  -14.31 1.82e+00 3.02e-01 6.18e+01
  angle pdb=" N   PHE M  92 "
        pdb=" CA  PHE M  92 "
        pdb=" C   PHE M  92 "
      ideal   model   delta    sigma   weight residual
     110.70  120.15   -9.45 1.55e+00 4.16e-01 3.72e+01
  ... (remaining 10765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.60: 4054
       16.60 -    33.20: 500
       33.20 -    49.79: 93
       49.79 -    66.39: 19
       66.39 -    82.99: 13
  Dihedral angle restraints: 4679
    sinusoidal: 1799
      harmonic: 2880
  Sorted by residual:
  dihedral pdb=" CA  TRP N  47 "
           pdb=" C   TRP N  47 "
           pdb=" N   ILE N  48 "
           pdb=" CA  ILE N  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -119.15  -60.85     0      5.00e+00 4.00e-02 1.48e+02
  dihedral pdb=" CA  TYR N 106 "
           pdb=" C   TYR N 106 "
           pdb=" N   PHE N 107 "
           pdb=" CA  PHE N 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.46   44.54     0      5.00e+00 4.00e-02 7.94e+01
  dihedral pdb=" N   SER M  95 "
           pdb=" C   SER M  95 "
           pdb=" CA  SER M  95 "
           pdb=" CB  SER M  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  143.24  -20.44     0      2.50e+00 1.60e-01 6.68e+01
  ... (remaining 4676 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.202: 1206
       0.202 -    0.404: 11
       0.404 -    0.606: 2
       0.606 -    0.807: 0
       0.807 -    1.009: 1
  Chirality restraints: 1220
  Sorted by residual:
  chirality pdb=" CA  SER M  95 "
            pdb=" N   SER M  95 "
            pdb=" C   SER M  95 "
            pdb=" CB  SER M  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.50    1.01 2.00e-01 2.50e+01 2.55e+01
  chirality pdb=" CA  ARG H  10 "
            pdb=" N   ARG H  10 "
            pdb=" C   ARG H  10 "
            pdb=" CB  ARG H  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.51e+00
  chirality pdb=" CA  GLN M  90 "
            pdb=" N   GLN M  90 "
            pdb=" C   GLN M  90 "
            pdb=" CB  GLN M  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.61e+00
  ... (remaining 1217 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 352 "    0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   HIS A 352 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   HIS A 352 "    0.027 2.00e-02 2.50e+03
        pdb=" N   GLU A 353 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY M  91 "   -0.017 2.00e-02 2.50e+03   3.50e-02 1.22e+01
        pdb=" C   GLY M  91 "    0.060 2.00e-02 2.50e+03
        pdb=" O   GLY M  91 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PHE M  92 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN M  90 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.55e+00
        pdb=" CD  GLN M  90 "    0.051 2.00e-02 2.50e+03
        pdb=" OE1 GLN M  90 "   -0.019 2.00e-02 2.50e+03
        pdb=" NE2 GLN M  90 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 262
        2.66 -     3.22: 6924
        3.22 -     3.78: 11285
        3.78 -     4.34: 13074
        4.34 -     4.90: 21101
  Nonbonded interactions: 52646
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 352 "
            pdb=" N   TYR A 355 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" OE1 GLN M  90 "
            pdb=" O   SER M 100 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER M  95 "
            pdb=" N   ASN M  96 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" N   GLN M  90 "
            pdb=" OE1 GLN M  90 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OH  TYR A 142 "
            pdb=" OD1 ASN A 163 "
     model   vdw
     2.232 3.040
  ... (remaining 52641 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.890
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.420
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
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      :  0.007   0.085   7940  Z= 0.357
  Angle     :  1.182  17.954  10774  Z= 0.659
  Chirality :  0.073   1.009   1220
  Planarity :  0.007   0.062   1374
  Dihedral  : 15.514  82.990   2841
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 14.56 %
    Favored  : 85.34 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 14.67 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.16 (0.20), residues: 989
  helix: -4.53 (0.26), residues: 67
  sheet: -3.23 (0.29), residues: 255
  loop : -3.61 (0.18), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  49 
 TYR   0.032   0.002   TYR M  87 
 PHE   0.030   0.002   PHE N 107 
 TRP   0.022   0.004   TRP N 110 
 HIS   0.008   0.002   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 ( 7938)
  covalent geometry    : angle       1.18184 (10770)
  SS BOND              : bond        0.00837 (    2)
  SS BOND              : angle       1.32502 (    4)
  hydrogen bonds       : bond        0.35204 (  114)
  hydrogen bonds       : angle      10.48511 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 234
  time to evaluate  : 0.291 
Fit side-chains
REVERT: H   29 LEU cc_start: 0.8711 (tt) cc_final: 0.8279 (mm)
REVERT: H   79 LYS cc_start: 0.9147 (mmtp) cc_final: 0.8858 (mmtm)
REVERT: H  101 MET cc_start: 0.8774 (mmm) cc_final: 0.8119 (mtt)
REVERT: L   35 TRP cc_start: 0.7424 (m-10) cc_final: 0.6905 (m-10)
REVERT: L   37 GLN cc_start: 0.9440 (tm-30) cc_final: 0.8951 (tm-30)
REVERT: L   38 GLN cc_start: 0.9113 (pp30) cc_final: 0.8691 (pm20)
REVERT: L   39 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8176 (tppt)
REVERT: L   42 GLN cc_start: 0.8744 (mp10) cc_final: 0.8481 (mp10)
REVERT: L   55 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7903 (tm-30)
REVERT: L   70 GLU cc_start: 0.8738 (pp20) cc_final: 0.8435 (mt-10)
REVERT: L   78 LEU cc_start: 0.8804 (mm) cc_final: 0.8372 (mt)
REVERT: L  101 ASN cc_start: 0.8794 (p0) cc_final: 0.8153 (p0)
REVERT: A  125 PHE cc_start: 0.8635 (m-10) cc_final: 0.8105 (m-10)
REVERT: A  147 MET cc_start: 0.7971 (tmm) cc_final: 0.7299 (tmm)
REVERT: A  181 TYR cc_start: 0.7255 (m-80) cc_final: 0.7048 (m-80)
REVERT: A  212 MET cc_start: 0.8189 (tpp) cc_final: 0.7910 (tpp)
REVERT: A  256 ASN cc_start: 0.9171 (p0) cc_final: 0.8941 (p0)
REVERT: A  272 GLU cc_start: 0.8672 (tp30) cc_final: 0.8079 (mt-10)
REVERT: A  279 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8276 (mmmm)
REVERT: A  313 LYS cc_start: 0.9362 (tppp) cc_final: 0.9033 (tppt)
REVERT: A  344 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7331 (mp0)
REVERT: A  382 TRP cc_start: 0.6197 (p-90) cc_final: 0.5726 (p-90)
REVERT: A  486 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: A  492 MET cc_start: 0.9320 (tmm) cc_final: 0.9105 (tmm)
REVERT: A  568 TYR cc_start: 0.8213 (m-10) cc_final: 0.8004 (m-80)
REVERT: A  589 GLN cc_start: 0.8418 (pm20) cc_final: 0.8188 (pm20)
REVERT: A  600 ASN cc_start: 0.9005 (t0) cc_final: 0.8574 (t0)
REVERT: A  603 HIS cc_start: 0.8715 (p-80) cc_final: 0.8480 (p-80)
REVERT: A  609 HIS cc_start: 0.8156 (m90) cc_final: 0.7621 (m90)
REVERT: A  635 ASN cc_start: 0.9020 (p0) cc_final: 0.8760 (m-40)
REVERT: A  653 ASN cc_start: 0.8909 (t0) cc_final: 0.8258 (t0)
REVERT: A  662 ARG cc_start: 0.8798 (ptm-80) cc_final: 0.7945 (ttm170)
REVERT: A  663 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8399 (tm-30)
REVERT: M    2 LEU cc_start: 0.8616 (pt) cc_final: 0.8385 (pp)
REVERT: M   22 LYS cc_start: 0.8271 (pttt) cc_final: 0.8026 (ptpp)
REVERT: M   88 CYS cc_start: 0.4654 (p) cc_final: 0.3654 (p)
REVERT: M   92 PHE cc_start: 0.4548 (OUTLIER) cc_final: 0.3814 (t80)
REVERT: N   22 CYS cc_start: 0.5443 (t) cc_final: 0.5187 (t)
REVERT: N   32 TYR cc_start: 0.7378 (m-80) cc_final: 0.6082 (m-80)
REVERT: N   34 MET cc_start: 0.9205 (mmp) cc_final: 0.8834 (mmp)
REVERT: N   36 TRP cc_start: 0.8163 (m100) cc_final: 0.7633 (m100)
REVERT: N   50 THR cc_start: 0.9180 (t) cc_final: 0.8456 (p)
REVERT: N   51 ILE cc_start: 0.9253 (tt) cc_final: 0.8866 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 236
  average time/residue: 0.0863
  time to fit residues: 27.1316
Evaluate side-chains
  188 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 185
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  352 HIS
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain N residue   58 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
H   2 GLN
H 100 ASN
A 256 ASN
** M  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 108 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.151115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106201 restraints weight = 15649.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.108773 restraints weight = 8145.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.110499 restraints weight = 4935.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.110838 restraints weight = 4450.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110829 restraints weight = 3942.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7940  Z= 0.137
  Angle     :  0.712   8.924  10774  Z= 0.375
  Chirality :  0.045   0.193   1220
  Planarity :  0.005   0.058   1374
  Dihedral  :  7.155  55.610   1105
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.73 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.21 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.53 (0.22), residues: 989
  helix: -3.37 (0.40), residues: 70
  sheet: -2.67 (0.29), residues: 278
  loop : -3.30 (0.20), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 646 
 TYR   0.020   0.001   TYR M  87 
 PHE   0.015   0.001   PHE N  92 
 TRP   0.017   0.002   TRP M  35 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7938)
  covalent geometry    : angle       0.71238 (10770)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       0.64469 (    4)
  hydrogen bonds       : bond        0.05038 (  114)
  hydrogen bonds       : angle       6.82832 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 0.233 
Fit side-chains
REVERT: H    4 VAL cc_start: 0.8702 (m) cc_final: 0.8468 (m)
REVERT: H   34 MET cc_start: 0.8768 (mmm) cc_final: 0.8166 (mmm)
REVERT: H   79 LYS cc_start: 0.9241 (mmtp) cc_final: 0.8911 (mmtm)
REVERT: H  101 MET cc_start: 0.8727 (mmm) cc_final: 0.8451 (mtm)
REVERT: L   35 TRP cc_start: 0.7198 (m-10) cc_final: 0.6878 (m-10)
REVERT: L   37 GLN cc_start: 0.9469 (tm-30) cc_final: 0.8908 (tm-30)
REVERT: L   38 GLN cc_start: 0.9081 (pp30) cc_final: 0.8604 (pm20)
REVERT: L   42 GLN cc_start: 0.8486 (mp10) cc_final: 0.8076 (mp10)
REVERT: L   78 LEU cc_start: 0.8926 (mm) cc_final: 0.8533 (mt)
REVERT: L   79 GLU cc_start: 0.8788 (tp30) cc_final: 0.8481 (tp30)
REVERT: L  101 ASN cc_start: 0.8891 (p0) cc_final: 0.8588 (p0)
REVERT: A  125 PHE cc_start: 0.8438 (m-10) cc_final: 0.7909 (m-10)
REVERT: A  147 MET cc_start: 0.7977 (tmm) cc_final: 0.7689 (tmm)
REVERT: A  313 LYS cc_start: 0.9313 (tppp) cc_final: 0.9079 (tppt)
REVERT: A  486 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: A  492 MET cc_start: 0.9289 (tmm) cc_final: 0.8956 (tmm)
REVERT: A  569 GLU cc_start: 0.8768 (pm20) cc_final: 0.8472 (pm20)
REVERT: A  589 GLN cc_start: 0.8509 (pm20) cc_final: 0.8258 (pm20)
REVERT: A  593 GLN cc_start: 0.9089 (pm20) cc_final: 0.8571 (pm20)
REVERT: A  609 HIS cc_start: 0.8130 (m90) cc_final: 0.7654 (m90)
REVERT: A  635 ASN cc_start: 0.9030 (p0) cc_final: 0.8706 (m-40)
REVERT: A  663 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8430 (tm-30)
REVERT: M    2 LEU cc_start: 0.8680 (pt) cc_final: 0.8452 (pp)
REVERT: M   36 TYR cc_start: 0.6926 (m-80) cc_final: 0.6038 (m-80)
REVERT: M   61 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7295 (ptt180)
REVERT: M   92 PHE cc_start: 0.4222 (OUTLIER) cc_final: 0.3568 (t80)
REVERT: N   34 MET cc_start: 0.9193 (mmp) cc_final: 0.8983 (mmp)
REVERT: N   36 TRP cc_start: 0.8087 (m100) cc_final: 0.7596 (m100)
REVERT: N   62 TRP cc_start: 0.8483 (m100) cc_final: 0.8139 (m100)
REVERT: N   71 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.6958 (ttm170)
  outliers start: 31
  outliers final: 15
  residues processed: 214
  average time/residue: 0.0815
  time to fit residues: 23.4521
Evaluate side-chains
  197 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain M residue   51 THR
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   77 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    0.3980
   chunk 54 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 78 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    3.6786

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

Flipped N/Q/H residues before XYZ refinement:
H   2 GLN
H 100 ASN
A 299 HIS
M  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.147649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.100190 restraints weight = 15466.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103258 restraints weight = 8730.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105292 restraints weight = 5999.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106591 restraints weight = 4645.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.107562 restraints weight = 3915.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7940  Z= 0.213
  Angle     :  0.744   9.292  10774  Z= 0.389
  Chirality :  0.046   0.172   1220
  Planarity :  0.005   0.052   1374
  Dihedral  :  6.949  54.756   1103
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.96 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.42 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.17 (0.23), residues: 989
  helix: -2.34 (0.53), residues: 70
  sheet: -2.36 (0.31), residues: 280
  loop : -3.18 (0.21), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  49 
 TYR   0.017   0.002   TYR M  87 
 PHE   0.025   0.002   PHE A 219 
 TRP   0.023   0.003   TRP A 300 
 HIS   0.005   0.001   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 7938)
  covalent geometry    : angle       0.74354 (10770)
  SS BOND              : bond        0.00577 (    2)
  SS BOND              : angle       1.41823 (    4)
  hydrogen bonds       : bond        0.05435 (  114)
  hydrogen bonds       : angle       6.71273 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 183
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8702 (mmm) cc_final: 0.8269 (mmm)
REVERT: H   46 GLU cc_start: 0.6608 (tt0) cc_final: 0.6205 (tt0)
REVERT: H   79 LYS cc_start: 0.9282 (mmtp) cc_final: 0.8952 (mmtm)
REVERT: L   37 GLN cc_start: 0.9432 (tm-30) cc_final: 0.8925 (tm-30)
REVERT: L   38 GLN cc_start: 0.9146 (pp30) cc_final: 0.7987 (pp30)
REVERT: L   39 LYS cc_start: 0.9006 (tppt) cc_final: 0.8429 (tppt)
REVERT: L   78 LEU cc_start: 0.8957 (mm) cc_final: 0.8737 (mm)
REVERT: L  101 ASN cc_start: 0.8751 (p0) cc_final: 0.8514 (p0)
REVERT: A   83 MET cc_start: 0.8628 (tpp) cc_final: 0.8310 (mmm)
REVERT: A  125 PHE cc_start: 0.8360 (m-10) cc_final: 0.7897 (m-10)
REVERT: A  147 MET cc_start: 0.8108 (tmm) cc_final: 0.7237 (tmm)
REVERT: A  181 TYR cc_start: 0.7590 (m-80) cc_final: 0.7285 (m-10)
REVERT: A  486 GLU cc_start: 0.8990 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: A  492 MET cc_start: 0.9277 (tmm) cc_final: 0.8975 (tmm)
REVERT: A  609 HIS cc_start: 0.8068 (m90) cc_final: 0.7654 (m90)
REVERT: A  635 ASN cc_start: 0.8989 (p0) cc_final: 0.8728 (m-40)
REVERT: A  647 ASP cc_start: 0.8790 (t0) cc_final: 0.8582 (t0)
REVERT: A  663 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8383 (tm-30)
REVERT: M   36 TYR cc_start: 0.7024 (m-80) cc_final: 0.6109 (m-80)
REVERT: M   61 ARG cc_start: 0.7667 (ptt180) cc_final: 0.7466 (ptt180)
REVERT: M   92 PHE cc_start: 0.4135 (OUTLIER) cc_final: 0.3428 (t80)
REVERT: N   34 MET cc_start: 0.9230 (mmp) cc_final: 0.8621 (mmp)
REVERT: N   36 TRP cc_start: 0.8048 (m100) cc_final: 0.7688 (m100)
REVERT: N   50 THR cc_start: 0.9058 (t) cc_final: 0.7979 (p)
REVERT: N   62 TRP cc_start: 0.8355 (m100) cc_final: 0.7916 (m100)
REVERT: N   71 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.6901 (ttm170)
REVERT: N  108 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8085 (m-40)
  outliers start: 46
  outliers final: 30
  residues processed: 207
  average time/residue: 0.0807
  time to fit residues: 22.7107
Evaluate side-chains
  209 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 177
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  352 HIS
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain M residue    3 VAL
Chi-restraints excluded: chain M residue   51 THR
Chi-restraints excluded: chain M residue   88 CYS
Chi-restraints excluded: chain M residue   89 GLN
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Chi-restraints excluded: chain N residue  108 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 76 optimal weight:   30.0000
   chunk 3 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
H   2 GLN
H 100 ASN
M  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.149965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102451 restraints weight = 15614.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.105671 restraints weight = 8595.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107832 restraints weight = 5827.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109191 restraints weight = 4459.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110227 restraints weight = 3738.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7940  Z= 0.149
  Angle     :  0.694   8.321  10774  Z= 0.360
  Chirality :  0.044   0.153   1220
  Planarity :  0.004   0.048   1374
  Dihedral  :  6.585  51.866   1103
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.74 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.82 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.90 (0.24), residues: 989
  helix: -1.80 (0.54), residues: 76
  sheet: -2.31 (0.32), residues: 276
  loop : -2.98 (0.21), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.011   0.001   TYR M  87 
 PHE   0.014   0.001   PHE A 219 
 TRP   0.014   0.002   TRP A 300 
 HIS   0.003   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7938)
  covalent geometry    : angle       0.69327 (10770)
  SS BOND              : bond        0.00638 (    2)
  SS BOND              : angle       1.72503 (    4)
  hydrogen bonds       : bond        0.04348 (  114)
  hydrogen bonds       : angle       6.30013 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 191
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   32 TYR cc_start: 0.8938 (m-10) cc_final: 0.8719 (m-80)
REVERT: H   34 MET cc_start: 0.8843 (mmm) cc_final: 0.8240 (mmm)
REVERT: H   46 GLU cc_start: 0.6460 (tt0) cc_final: 0.6060 (tt0)
REVERT: H   79 LYS cc_start: 0.9272 (mmtp) cc_final: 0.8960 (mmtm)
REVERT: H  101 MET cc_start: 0.8058 (mtt) cc_final: 0.7820 (mtm)
REVERT: L   35 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.6716 (m-10)
REVERT: L   37 GLN cc_start: 0.9370 (tm-30) cc_final: 0.8885 (tm-30)
REVERT: L   38 GLN cc_start: 0.9044 (pp30) cc_final: 0.7975 (pp30)
REVERT: L   39 LYS cc_start: 0.8870 (tppt) cc_final: 0.8358 (tppt)
REVERT: L  101 ASN cc_start: 0.8782 (p0) cc_final: 0.8542 (p0)
REVERT: A   83 MET cc_start: 0.8536 (tpp) cc_final: 0.8287 (mmm)
REVERT: A  125 PHE cc_start: 0.8348 (m-10) cc_final: 0.7961 (m-10)
REVERT: A  147 MET cc_start: 0.8007 (tmm) cc_final: 0.7127 (tmm)
REVERT: A  486 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: A  492 MET cc_start: 0.9321 (tmm) cc_final: 0.8998 (tmm)
REVERT: A  609 HIS cc_start: 0.8048 (m90) cc_final: 0.7660 (m90)
REVERT: A  635 ASN cc_start: 0.8976 (p0) cc_final: 0.8721 (m-40)
REVERT: A  647 ASP cc_start: 0.8793 (t0) cc_final: 0.8581 (t0)
REVERT: A  653 ASN cc_start: 0.8920 (t0) cc_final: 0.8246 (t0)
REVERT: A  663 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: M   36 TYR cc_start: 0.6957 (m-80) cc_final: 0.6246 (m-80)
REVERT: M   69 THR cc_start: 0.5997 (OUTLIER) cc_final: 0.5775 (m)
REVERT: M   77 ASP cc_start: 0.8622 (m-30) cc_final: 0.8287 (m-30)
REVERT: M   92 PHE cc_start: 0.3910 (OUTLIER) cc_final: 0.3242 (t80)
REVERT: M   99 ASN cc_start: 0.8933 (t0) cc_final: 0.8608 (t0)
REVERT: N   34 MET cc_start: 0.9171 (mmp) cc_final: 0.8553 (mmp)
REVERT: N   36 TRP cc_start: 0.8015 (m100) cc_final: 0.7604 (m100)
REVERT: N   50 THR cc_start: 0.9111 (t) cc_final: 0.8080 (p)
REVERT: N   71 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.6821 (ttm170)
REVERT: N  108 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7970 (m-40)
  outliers start: 40
  outliers final: 28
  residues processed: 212
  average time/residue: 0.0743
  time to fit residues: 21.6045
Evaluate side-chains
  219 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain M residue  106 LYS
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Chi-restraints excluded: chain N residue  108 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 94 optimal weight:   20.0000
   chunk 42 optimal weight:    0.0070
   chunk 97 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.9202

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

Flipped N/Q/H residues before XYZ refinement:
H   2 GLN
H 100 ASN
A 264 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.152063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.103499 restraints weight = 16491.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.107095 restraints weight = 8503.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109478 restraints weight = 5639.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.110974 restraints weight = 4312.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.112048 restraints weight = 3618.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7940  Z= 0.107
  Angle     :  0.647   9.476  10774  Z= 0.333
  Chirality :  0.043   0.145   1220
  Planarity :  0.004   0.047   1374
  Dihedral  :  5.854  46.886   1103
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.02 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.82 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.58 (0.25), residues: 989
  helix: -1.14 (0.59), residues: 72
  sheet: -2.09 (0.32), residues: 272
  loop : -2.81 (0.22), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.011   0.001   TYR M  87 
 PHE   0.008   0.001   PHE A 219 
 TRP   0.015   0.002   TRP M  35 
 HIS   0.001   0.000   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 7938)
  covalent geometry    : angle       0.64626 (10770)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       1.40307 (    4)
  hydrogen bonds       : bond        0.03564 (  114)
  hydrogen bonds       : angle       5.76071 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 202
  time to evaluate  : 0.274 
Fit side-chains
REVERT: H    2 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.9170 (pm20)
REVERT: H    6 GLU cc_start: 0.8083 (pm20) cc_final: 0.7840 (pm20)
REVERT: H   34 MET cc_start: 0.8979 (mmm) cc_final: 0.8706 (mmm)
REVERT: H   79 LYS cc_start: 0.9184 (mmtp) cc_final: 0.8876 (mmtm)
REVERT: H  101 MET cc_start: 0.7867 (mtt) cc_final: 0.7627 (mtm)
REVERT: L   35 TRP cc_start: 0.7164 (m-10) cc_final: 0.6524 (m-10)
REVERT: L   37 GLN cc_start: 0.9340 (tm-30) cc_final: 0.8906 (tm-30)
REVERT: L   38 GLN cc_start: 0.8938 (pp30) cc_final: 0.8559 (pm20)
REVERT: L   99 LEU cc_start: 0.8862 (mp) cc_final: 0.8603 (mp)
REVERT: L  101 ASN cc_start: 0.8783 (p0) cc_final: 0.8468 (p0)
REVERT: A   83 MET cc_start: 0.8333 (tpp) cc_final: 0.8080 (mmm)
REVERT: A  147 MET cc_start: 0.7765 (tmm) cc_final: 0.7380 (tmm)
REVERT: A  181 TYR cc_start: 0.7443 (m-80) cc_final: 0.7104 (m-10)
REVERT: A  231 GLU cc_start: 0.8476 (mp0) cc_final: 0.8232 (mp0)
REVERT: A  272 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8308 (tp30)
REVERT: A  344 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7376 (mp0)
REVERT: A  486 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: A  492 MET cc_start: 0.9269 (tmm) cc_final: 0.8945 (tmm)
REVERT: A  569 GLU cc_start: 0.8892 (pm20) cc_final: 0.8626 (pm20)
REVERT: A  609 HIS cc_start: 0.8008 (m90) cc_final: 0.7608 (m90)
REVERT: A  635 ASN cc_start: 0.8972 (p0) cc_final: 0.8730 (m-40)
REVERT: A  647 ASP cc_start: 0.8725 (t0) cc_final: 0.8495 (t0)
REVERT: A  653 ASN cc_start: 0.8930 (t0) cc_final: 0.8468 (t0)
REVERT: A  663 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: M   36 TYR cc_start: 0.7062 (m-80) cc_final: 0.6283 (m-80)
REVERT: M   42 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7642 (tp-100)
REVERT: M   69 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5556 (m)
REVERT: M   92 PHE cc_start: 0.4092 (OUTLIER) cc_final: 0.3813 (t80)
REVERT: M   99 ASN cc_start: 0.8969 (t0) cc_final: 0.8638 (t0)
REVERT: N   34 MET cc_start: 0.8988 (mmp) cc_final: 0.8731 (mmp)
REVERT: N   36 TRP cc_start: 0.7826 (m100) cc_final: 0.7423 (m100)
REVERT: N   71 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6769 (ttm170)
REVERT: N   95 ARG cc_start: 0.6886 (ttp-170) cc_final: 0.6611 (tmm160)
REVERT: N  108 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7546 (m-40)
  outliers start: 43
  outliers final: 26
  residues processed: 220
  average time/residue: 0.0779
  time to fit residues: 23.4290
Evaluate side-chains
  221 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 GLN
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   78 LEU
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  352 HIS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   88 CYS
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Chi-restraints excluded: chain N residue  108 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 75 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0020
   chunk 4 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
H   2 GLN
H 100 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.153166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.104591 restraints weight = 16584.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.108230 restraints weight = 8539.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.110629 restraints weight = 5684.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112278 restraints weight = 4299.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.113376 restraints weight = 3566.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7940  Z= 0.108
  Angle     :  0.659   9.753  10774  Z= 0.336
  Chirality :  0.043   0.165   1220
  Planarity :  0.004   0.046   1374
  Dihedral  :  5.528  40.254   1103
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.12 %
    Favored  : 88.88 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 24.45 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.41 (0.24), residues: 989
  helix: -0.89 (0.59), residues: 73
  sheet: -1.91 (0.33), residues: 261
  loop : -2.74 (0.21), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.016   0.001   TYR H  32 
 PHE   0.009   0.001   PHE H  27 
 TRP   0.012   0.001   TRP M  35 
 HIS   0.001   0.000   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7938)
  covalent geometry    : angle       0.65893 (10770)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       1.44495 (    4)
  hydrogen bonds       : bond        0.03329 (  114)
  hydrogen bonds       : angle       5.49864 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 202
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8986 (mmm) cc_final: 0.8728 (mmm)
REVERT: H   46 GLU cc_start: 0.5859 (tt0) cc_final: 0.5221 (tt0)
REVERT: H   79 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8833 (mmtm)
REVERT: L   35 TRP cc_start: 0.7078 (m-10) cc_final: 0.6350 (m-10)
REVERT: L   37 GLN cc_start: 0.9345 (tm-30) cc_final: 0.8902 (tm-30)
REVERT: L   38 GLN cc_start: 0.8897 (pp30) cc_final: 0.8518 (pp30)
REVERT: L   39 LYS cc_start: 0.8772 (tppt) cc_final: 0.8475 (tptt)
REVERT: L   55 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: A  102 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8106 (tp)
REVERT: A  147 MET cc_start: 0.7742 (tmm) cc_final: 0.6850 (tmm)
REVERT: A  231 GLU cc_start: 0.8303 (mp0) cc_final: 0.8079 (mp0)
REVERT: A  344 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7441 (mp0)
REVERT: A  486 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8378 (tm-30)
REVERT: A  492 MET cc_start: 0.9257 (tmm) cc_final: 0.8974 (tmm)
REVERT: A  501 ASN cc_start: 0.8771 (p0) cc_final: 0.8054 (p0)
REVERT: A  569 GLU cc_start: 0.8901 (pm20) cc_final: 0.8641 (pm20)
REVERT: A  609 HIS cc_start: 0.8079 (m90) cc_final: 0.7683 (m90)
REVERT: A  635 ASN cc_start: 0.8888 (p0) cc_final: 0.8648 (m-40)
REVERT: A  647 ASP cc_start: 0.8702 (t0) cc_final: 0.8465 (t0)
REVERT: A  653 ASN cc_start: 0.8933 (t0) cc_final: 0.8640 (t0)
REVERT: A  663 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8689 (tm-30)
REVERT: M   36 TYR cc_start: 0.7070 (m-80) cc_final: 0.6245 (m-80)
REVERT: M   69 THR cc_start: 0.5708 (OUTLIER) cc_final: 0.5339 (m)
REVERT: M   99 ASN cc_start: 0.8960 (t0) cc_final: 0.8738 (t0)
REVERT: N   34 MET cc_start: 0.8966 (mmp) cc_final: 0.8699 (mmp)
REVERT: N   36 TRP cc_start: 0.7531 (m100) cc_final: 0.7075 (m100)
REVERT: N   71 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6775 (ttm170)
REVERT: N  108 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7182 (m-40)
  outliers start: 41
  outliers final: 30
  residues processed: 216
  average time/residue: 0.0754
  time to fit residues: 22.3230
Evaluate side-chains
  227 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 194
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain N residue    4 VAL
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   59 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Chi-restraints excluded: chain N residue  108 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 88 optimal weight:    0.4980
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.152081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.103151 restraints weight = 16570.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106802 restraints weight = 8406.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.109179 restraints weight = 5523.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.110752 restraints weight = 4208.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.111763 restraints weight = 3530.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7940  Z= 0.140
  Angle     :  0.683  11.770  10774  Z= 0.346
  Chirality :  0.043   0.156   1220
  Planarity :  0.004   0.042   1374
  Dihedral  :  5.536  38.309   1101
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.93 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 24.21 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.32 (0.25), residues: 989
  helix: -0.61 (0.58), residues: 72
  sheet: -1.88 (0.33), residues: 258
  loop : -2.69 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.013   0.001   TYR M  87 
 PHE   0.014   0.001   PHE A 219 
 TRP   0.027   0.003   TRP N  47 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7938)
  covalent geometry    : angle       0.68227 (10770)
  SS BOND              : bond        0.00352 (    2)
  SS BOND              : angle       1.45948 (    4)
  hydrogen bonds       : bond        0.03785 (  114)
  hydrogen bonds       : angle       5.56593 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8839 (mmm) cc_final: 0.8543 (mmm)
REVERT: H   46 GLU cc_start: 0.6069 (tt0) cc_final: 0.5388 (tt0)
REVERT: H   47 TYR cc_start: 0.7904 (t80) cc_final: 0.7545 (t80)
REVERT: L   35 TRP cc_start: 0.7532 (OUTLIER) cc_final: 0.6676 (m-10)
REVERT: L   37 GLN cc_start: 0.9401 (tm-30) cc_final: 0.8964 (tm-30)
REVERT: L   38 GLN cc_start: 0.9013 (pp30) cc_final: 0.8501 (pp30)
REVERT: A  147 MET cc_start: 0.7921 (tmm) cc_final: 0.7021 (tmm)
REVERT: A  181 TYR cc_start: 0.7302 (m-80) cc_final: 0.7039 (m-80)
REVERT: A  344 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7437 (mp0)
REVERT: A  486 GLU cc_start: 0.8866 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: A  492 MET cc_start: 0.9250 (tmm) cc_final: 0.8975 (tmm)
REVERT: A  569 GLU cc_start: 0.8858 (pm20) cc_final: 0.8599 (pm20)
REVERT: A  609 HIS cc_start: 0.8088 (m90) cc_final: 0.7726 (m90)
REVERT: A  647 ASP cc_start: 0.8677 (t0) cc_final: 0.8433 (t0)
REVERT: A  653 ASN cc_start: 0.8941 (t0) cc_final: 0.8680 (t0)
REVERT: A  663 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: M   36 TYR cc_start: 0.6982 (m-80) cc_final: 0.6159 (m-80)
REVERT: M   42 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7549 (tp-100)
REVERT: M   69 THR cc_start: 0.5926 (OUTLIER) cc_final: 0.5560 (m)
REVERT: M   92 PHE cc_start: 0.4260 (OUTLIER) cc_final: 0.3894 (t80)
REVERT: M   99 ASN cc_start: 0.8995 (t0) cc_final: 0.8754 (t0)
REVERT: N   36 TRP cc_start: 0.7642 (m100) cc_final: 0.7314 (m100)
REVERT: N   71 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7268 (ttm170)
  outliers start: 45
  outliers final: 33
  residues processed: 219
  average time/residue: 0.0830
  time to fit residues: 24.6791
Evaluate side-chains
  223 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 187
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  352 HIS
Chi-restraints excluded: chain A residue  382 TRP
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 19 optimal weight:    0.0050
   chunk 85 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0970
   chunk 46 optimal weight:    0.8980
   chunk 94 optimal weight:   20.0000
   chunk 95 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN
** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.153864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105046 restraints weight = 16627.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.108776 restraints weight = 8369.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.111221 restraints weight = 5465.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.112704 restraints weight = 4143.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.113777 restraints weight = 3478.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7940  Z= 0.114
  Angle     :  0.696  11.325  10774  Z= 0.347
  Chirality :  0.043   0.180   1220
  Planarity :  0.004   0.038   1374
  Dihedral  :  5.386  37.643   1101
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 25.49 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.25), residues: 989
  helix: -0.24 (0.61), residues: 72
  sheet: -1.84 (0.33), residues: 255
  loop : -2.68 (0.22), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  49 
 TYR   0.011   0.001   TYR M  87 
 PHE   0.008   0.001   PHE A 219 
 TRP   0.022   0.002   TRP N  47 
 HIS   0.001   0.000   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7938)
  covalent geometry    : angle       0.69509 (10770)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       1.61421 (    4)
  hydrogen bonds       : bond        0.03320 (  114)
  hydrogen bonds       : angle       5.30579 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 195
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8868 (mmm) cc_final: 0.8573 (mmm)
REVERT: H   46 GLU cc_start: 0.6085 (tt0) cc_final: 0.5444 (tm-30)
REVERT: H   47 TYR cc_start: 0.7731 (t80) cc_final: 0.7345 (t80)
REVERT: H   93 CYS cc_start: 0.7880 (m) cc_final: 0.7601 (t)
REVERT: L   27 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8619 (mp10)
REVERT: L   37 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8915 (tm-30)
REVERT: L   38 GLN cc_start: 0.8855 (pp30) cc_final: 0.8388 (pm20)
REVERT: A  147 MET cc_start: 0.7874 (tmm) cc_final: 0.6984 (tmm)
REVERT: A  181 TYR cc_start: 0.7267 (m-80) cc_final: 0.7017 (m-80)
REVERT: A  344 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7328 (mp0)
REVERT: A  486 GLU cc_start: 0.8837 (tm-30) cc_final: 0.7874 (tm-30)
REVERT: A  492 MET cc_start: 0.9218 (tmm) cc_final: 0.8899 (tmm)
REVERT: A  501 ASN cc_start: 0.8830 (p0) cc_final: 0.8071 (p0)
REVERT: A  569 GLU cc_start: 0.8832 (pm20) cc_final: 0.8572 (pm20)
REVERT: A  609 HIS cc_start: 0.8052 (m90) cc_final: 0.7695 (m90)
REVERT: A  647 ASP cc_start: 0.8658 (t0) cc_final: 0.8411 (t0)
REVERT: A  653 ASN cc_start: 0.8919 (t0) cc_final: 0.8651 (t0)
REVERT: A  663 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: M   36 TYR cc_start: 0.6909 (m-80) cc_final: 0.6068 (m-80)
REVERT: M   42 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7635 (tp-100)
REVERT: M   69 THR cc_start: 0.5865 (OUTLIER) cc_final: 0.5504 (m)
REVERT: M   92 PHE cc_start: 0.4284 (OUTLIER) cc_final: 0.3849 (t80)
REVERT: M   99 ASN cc_start: 0.8973 (t0) cc_final: 0.8594 (t0)
REVERT: N   36 TRP cc_start: 0.7478 (m100) cc_final: 0.7142 (m100)
REVERT: N   62 TRP cc_start: 0.7497 (m-10) cc_final: 0.6743 (p-90)
REVERT: N   71 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7355 (ttm170)
  outliers start: 36
  outliers final: 32
  residues processed: 211
  average time/residue: 0.0772
  time to fit residues: 22.2768
Evaluate side-chains
  220 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 186
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:   20.0000
   chunk 65 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0470
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 70 optimal weight:    8.9990
   chunk 19 optimal weight:    0.5980
   chunk 32 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    3.1284

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN
N 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.147440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.102257 restraints weight = 16650.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.104110 restraints weight = 9005.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.105677 restraints weight = 5938.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.105961 restraints weight = 5487.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.105879 restraints weight = 4765.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7940  Z= 0.186
  Angle     :  0.744  10.603  10774  Z= 0.376
  Chirality :  0.045   0.165   1220
  Planarity :  0.004   0.041   1374
  Dihedral  :  5.793  38.200   1101
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.55 %
    Favored  : 86.45 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 24.91 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.32 (0.25), residues: 989
  helix: -0.33 (0.64), residues: 64
  sheet: -1.87 (0.32), residues: 267
  loop : -2.71 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG N  95 
 TYR   0.014   0.001   TYR M  87 
 PHE   0.018   0.001   PHE A 219 
 TRP   0.019   0.003   TRP N 110 
 HIS   0.004   0.001   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7938)
  covalent geometry    : angle       0.74368 (10770)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       1.56352 (    4)
  hydrogen bonds       : bond        0.04251 (  114)
  hydrogen bonds       : angle       5.67122 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 187
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8789 (mmm) cc_final: 0.8320 (mmm)
REVERT: H   46 GLU cc_start: 0.6196 (tt0) cc_final: 0.5522 (tt0)
REVERT: H   47 TYR cc_start: 0.7906 (t80) cc_final: 0.7545 (t80)
REVERT: L   35 TRP cc_start: 0.7559 (OUTLIER) cc_final: 0.6408 (m-10)
REVERT: L   37 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8885 (tm-30)
REVERT: A  147 MET cc_start: 0.7645 (tmm) cc_final: 0.6773 (tmm)
REVERT: A  181 TYR cc_start: 0.7361 (m-80) cc_final: 0.7034 (m-10)
REVERT: A  344 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7655 (mt-10)
REVERT: A  492 MET cc_start: 0.9326 (tmm) cc_final: 0.9036 (tmm)
REVERT: A  569 GLU cc_start: 0.8965 (pm20) cc_final: 0.8723 (pm20)
REVERT: A  609 HIS cc_start: 0.8193 (m90) cc_final: 0.7843 (m90)
REVERT: A  647 ASP cc_start: 0.8760 (t0) cc_final: 0.8519 (t0)
REVERT: A  653 ASN cc_start: 0.8972 (t0) cc_final: 0.8399 (t0)
REVERT: A  663 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: M   36 TYR cc_start: 0.6958 (m-80) cc_final: 0.6006 (m-80)
REVERT: M   69 THR cc_start: 0.5554 (OUTLIER) cc_final: 0.5197 (m)
REVERT: M   92 PHE cc_start: 0.4098 (OUTLIER) cc_final: 0.3730 (t80)
REVERT: M   99 ASN cc_start: 0.9037 (t0) cc_final: 0.8799 (t0)
REVERT: N   36 TRP cc_start: 0.7456 (m100) cc_final: 0.7158 (m100)
REVERT: N   71 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7096 (ttm170)
  outliers start: 43
  outliers final: 35
  residues processed: 211
  average time/residue: 0.0776
  time to fit residues: 22.4383
Evaluate side-chains
  221 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  382 TRP
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 96 optimal weight:    9.9990
   chunk 68 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   chunk 36 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    4.3786

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN
A  77 HIS
A 669 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.145788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097345 restraints weight = 16237.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.100513 restraints weight = 8987.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102590 restraints weight = 6149.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103958 restraints weight = 4772.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104920 restraints weight = 4017.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7940  Z= 0.243
  Angle     :  0.810  10.107  10774  Z= 0.414
  Chirality :  0.047   0.194   1220
  Planarity :  0.005   0.041   1374
  Dihedral  :  6.347  39.477   1101
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.46 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 25.73 %
    Favored  : 69.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.25), residues: 989
  helix: -0.89 (0.60), residues: 70
  sheet: -2.00 (0.32), residues: 267
  loop : -2.80 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG N  95 
 TYR   0.017   0.002   TYR M  87 
 PHE   0.019   0.002   PHE A 219 
 TRP   0.025   0.004   TRP A 300 
 HIS   0.006   0.001   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 7938)
  covalent geometry    : angle       0.80964 (10770)
  SS BOND              : bond        0.00651 (    2)
  SS BOND              : angle       1.62011 (    4)
  hydrogen bonds       : bond        0.04775 (  114)
  hydrogen bonds       : angle       6.06697 (  318)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 182
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8804 (mmm) cc_final: 0.8343 (mmm)
REVERT: H   46 GLU cc_start: 0.6215 (tt0) cc_final: 0.5482 (tt0)
REVERT: H   47 TYR cc_start: 0.7956 (t80) cc_final: 0.7595 (t80)
REVERT: H   79 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8913 (mmtm)
REVERT: L   37 GLN cc_start: 0.9375 (tm-30) cc_final: 0.8855 (tm-30)
REVERT: A   83 MET cc_start: 0.8880 (tpp) cc_final: 0.8414 (mmm)
REVERT: A  147 MET cc_start: 0.7726 (tmm) cc_final: 0.7124 (tmm)
REVERT: A  181 TYR cc_start: 0.7429 (m-80) cc_final: 0.7123 (m-10)
REVERT: A  492 MET cc_start: 0.9291 (tmm) cc_final: 0.9026 (tmm)
REVERT: A  550 MET cc_start: 0.8904 (mpp) cc_final: 0.8626 (mpp)
REVERT: A  569 GLU cc_start: 0.8894 (pm20) cc_final: 0.8674 (pm20)
REVERT: A  609 HIS cc_start: 0.8118 (m90) cc_final: 0.7776 (m90)
REVERT: A  647 ASP cc_start: 0.8790 (t0) cc_final: 0.8534 (t0)
REVERT: A  653 ASN cc_start: 0.8976 (t0) cc_final: 0.8466 (t0)
REVERT: A  663 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8484 (tm-30)
REVERT: M   36 TYR cc_start: 0.6790 (m-80) cc_final: 0.5891 (m-80)
REVERT: M   69 THR cc_start: 0.5957 (OUTLIER) cc_final: 0.5707 (m)
REVERT: M   92 PHE cc_start: 0.4047 (OUTLIER) cc_final: 0.3710 (t80)
REVERT: M   99 ASN cc_start: 0.9070 (t0) cc_final: 0.8817 (t0)
REVERT: N   36 TRP cc_start: 0.7524 (m100) cc_final: 0.7251 (m100)
REVERT: N   71 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7042 (ttm170)
  outliers start: 44
  outliers final: 33
  residues processed: 208
  average time/residue: 0.0768
  time to fit residues: 22.1776
Evaluate side-chains
  215 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  382 TRP
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   69 THR
Chi-restraints excluded: chain M residue   92 PHE
Chi-restraints excluded: chain M residue   98 TYR
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   58 TYR
Chi-restraints excluded: chain N residue   76 VAL
Chi-restraints excluded: chain N residue   77 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0270
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:    0.2980
   chunk 97 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    1.4242

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN
M   6 GLN
N 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.150179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101801 restraints weight = 16255.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.105195 restraints weight = 8746.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.107392 restraints weight = 5882.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.108825 restraints weight = 4553.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.109866 restraints weight = 3853.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7940  Z= 0.129
  Angle     :  0.772  11.296  10774  Z= 0.386
  Chirality :  0.045   0.203   1220
  Planarity :  0.004   0.042   1374
  Dihedral  :  5.801  39.257   1101
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.31 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.31 (0.25), residues: 989
  helix: -0.43 (0.59), residues: 76
  sheet: -1.89 (0.32), residues: 265
  loop : -2.72 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N  95 
 TYR   0.020   0.001   TYR M  87 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.025   0.003   TRP N  47 
 HIS   0.002   0.000   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7938)
  covalent geometry    : angle       0.76836 (10770)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       3.70592 (    4)
  hydrogen bonds       : bond        0.03508 (  114)
  hydrogen bonds       : angle       5.64692 (  318)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1585.58 seconds
wall clock time: 28 minutes 0.44 seconds (1680.44 seconds total)