Starting phenix.real_space_refine
on Wed Mar 12 12:25:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fbi_31515/03_2025/7fbi_31515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fbi_31515/03_2025/7fbi_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2025/7fbi_31515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2025/7fbi_31515.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2025/7fbi_31515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fbi_31515/03_2025/7fbi_31515.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.76, per 1000 atoms: 0.61
  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: 1.76
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.03
  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: 2.00

  Time building geometry restraints manager: 2.11 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:             1.640
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.390
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.280
-------------------------------------------------------------------------------
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   7938  Z= 0.451
  Angle     :  1.182  17.954  10770  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.022   0.004   TRP N 110 
 HIS   0.008   0.002   HIS A 603 
 PHE   0.030   0.002   PHE N 107 
 TYR   0.032   0.002   TYR M  87 
 ARG   0.008   0.001   ARG A  49 

*********************** 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  : 0.829 
Fit side-chains
REVERT: H    5 LYS cc_start: 0.9268 (mmmt) cc_final: 0.9061 (mmmt)
REVERT: H   29 LEU cc_start: 0.8711 (tt) cc_final: 0.8284 (mm)
REVERT: H   79 LYS cc_start: 0.9147 (mmtp) cc_final: 0.8855 (mmtm)
REVERT: H  101 MET cc_start: 0.8774 (mmm) cc_final: 0.8122 (mtt)
REVERT: L   35 TRP cc_start: 0.7424 (m-10) cc_final: 0.6904 (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: 0.8690 (pm20)
REVERT: L   39 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8175 (tppt)
REVERT: L   42 GLN cc_start: 0.8744 (mp10) cc_final: 0.8480 (mp10)
REVERT: L   55 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: L   63 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8032 (mtm110)
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: 0.8378 (mt)
REVERT: L  101 ASN cc_start: 0.8794 (p0) cc_final: 0.8154 (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: 0.7332 (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: 0.8575 (t0)
REVERT: A  603 HIS cc_start: 0.8715 (p-80) cc_final: 0.8481 (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: 0.8398 (tm-30)
REVERT: M    2 LEU cc_start: 0.8616 (pt) cc_final: 0.8386 (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: 0.3653 (p)
REVERT: M   92 PHE cc_start: 0.4548 (OUTLIER) cc_final: 0.3828 (t80)
REVERT: N   22 CYS cc_start: 0.5443 (t) cc_final: 0.5185 (t)
REVERT: N   32 TYR cc_start: 0.7378 (m-80) cc_final: 0.5917 (m-80)
REVERT: N   34 MET cc_start: 0.9205 (mmp) cc_final: 0.8833 (mmp)
REVERT: N   36 TRP cc_start: 0.8163 (m100) cc_final: 0.7632 (m100)
REVERT: N   50 THR cc_start: 0.9180 (t) cc_final: 0.8457 (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: 0.2205
  time to fit residues: 68.0289
Evaluate side-chains
  190 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 187
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
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 82 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.151543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.104555 restraints weight = 15365.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.107757 restraints weight = 8535.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109752 restraints weight = 5804.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7938  Z= 0.188
  Angle     :  0.716   8.882  10770  Z= 0.378
  Chirality :  0.045   0.189   1220
  Planarity :  0.005   0.057   1374
  Dihedral  :  7.164  55.582   1105
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.73 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.86 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.52 (0.22), residues: 989
  helix: -3.36 (0.40), residues: 70
  sheet: -2.62 (0.30), residues: 270
  loop : -3.32 (0.20), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP M  35 
 HIS   0.002   0.000   HIS A 316 
 PHE   0.015   0.001   PHE N  92 
 TYR   0.021   0.001   TYR M  87 
 ARG   0.008   0.000   ARG A 646 

*********************** 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
  237 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 0.985 
Fit side-chains
REVERT: H    6 GLU cc_start: 0.7989 (mp0) cc_final: 0.7373 (mp0)
REVERT: H   12 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7700 (t)
REVERT: H   79 LYS cc_start: 0.9243 (mmtp) cc_final: 0.8916 (mmtm)
REVERT: H  101 MET cc_start: 0.8727 (mmm) cc_final: 0.8458 (mtm)
REVERT: L   35 TRP cc_start: 0.7166 (m-10) cc_final: 0.6832 (m-10)
REVERT: L   37 GLN cc_start: 0.9442 (tm-30) cc_final: 0.8876 (tm-30)
REVERT: L   38 GLN cc_start: 0.9067 (pp30) cc_final: 0.8593 (pm20)
REVERT: L   42 GLN cc_start: 0.8505 (mp10) cc_final: 0.8262 (mp10)
REVERT: L   55 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7886 (tm-30)
REVERT: L   78 LEU cc_start: 0.8938 (mm) cc_final: 0.8546 (mt)
REVERT: L   79 GLU cc_start: 0.8789 (tp30) cc_final: 0.8486 (tp30)
REVERT: L  101 ASN cc_start: 0.8896 (p0) cc_final: 0.8570 (p0)
REVERT: A  125 PHE cc_start: 0.8502 (m-10) cc_final: 0.7962 (m-10)
REVERT: A  147 MET cc_start: 0.8048 (tmm) cc_final: 0.7765 (tmm)
REVERT: A  313 LYS cc_start: 0.9318 (tppp) cc_final: 0.9081 (tppt)
REVERT: A  352 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7397 (t70)
REVERT: A  486 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8472 (tm-30)
REVERT: A  492 MET cc_start: 0.9297 (tmm) cc_final: 0.8963 (tmm)
REVERT: A  569 GLU cc_start: 0.8764 (pm20) cc_final: 0.8476 (pm20)
REVERT: A  589 GLN cc_start: 0.8493 (pm20) cc_final: 0.8203 (pm20)
REVERT: A  593 GLN cc_start: 0.9081 (pm20) cc_final: 0.8594 (pm20)
REVERT: A  609 HIS cc_start: 0.8147 (m90) cc_final: 0.7668 (m90)
REVERT: A  635 ASN cc_start: 0.9027 (p0) cc_final: 0.8698 (m-40)
REVERT: A  663 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: M    2 LEU cc_start: 0.8673 (pt) cc_final: 0.8452 (pp)
REVERT: M   36 TYR cc_start: 0.6912 (m-80) cc_final: 0.6008 (m-80)
REVERT: M   61 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7291 (ptt180)
REVERT: M   92 PHE cc_start: 0.4305 (OUTLIER) cc_final: 0.3610 (t80)
REVERT: N   34 MET cc_start: 0.9175 (mmp) cc_final: 0.8612 (mmp)
REVERT: N   36 TRP cc_start: 0.8071 (m100) cc_final: 0.7576 (m100)
REVERT: N   50 THR cc_start: 0.9112 (t) cc_final: 0.8180 (p)
REVERT: N   62 TRP cc_start: 0.8455 (m100) cc_final: 0.8129 (m100)
  outliers start: 33
  outliers final: 17
  residues processed: 219
  average time/residue: 0.2297
  time to fit residues: 67.0289
Evaluate side-chains
  205 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
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   49 ARG
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  352 HIS
Chi-restraints excluded: chain A residue  484 CYS
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 30 optimal weight:   20.0000
   chunk 22 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 67 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 87 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.148048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.108114 restraints weight = 16202.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107776 restraints weight = 8149.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.108485 restraints weight = 6949.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7938  Z= 0.243
  Angle     :  0.710   9.095  10770  Z= 0.369
  Chirality :  0.045   0.166   1220
  Planarity :  0.004   0.053   1374
  Dihedral  :  6.864  53.138   1105
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.30 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.04 (0.24), residues: 989
  helix: -2.10 (0.53), residues: 76
  sheet: -2.34 (0.32), residues: 275
  loop : -3.09 (0.21), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 300 
 HIS   0.004   0.001   HIS A 316 
 PHE   0.021   0.001   PHE A 219 
 TYR   0.016   0.002   TYR M  87 
 ARG   0.003   0.000   ARG H  10 

*********************** 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
  236 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.7975 (mp0) cc_final: 0.7287 (mp0)
REVERT: H   34 MET cc_start: 0.8741 (mmm) cc_final: 0.8315 (mmm)
REVERT: H   46 GLU cc_start: 0.6768 (tt0) cc_final: 0.6519 (tt0)
REVERT: H   79 LYS cc_start: 0.9244 (mmtp) cc_final: 0.8918 (mmtm)
REVERT: H  101 MET cc_start: 0.8667 (mmm) cc_final: 0.8440 (mtm)
REVERT: L   37 GLN cc_start: 0.9440 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: L   38 GLN cc_start: 0.9075 (pp30) cc_final: 0.8806 (pm20)
REVERT: L   39 LYS cc_start: 0.8907 (tppt) cc_final: 0.8434 (tppt)
REVERT: L   42 GLN cc_start: 0.8456 (mp10) cc_final: 0.8103 (mp10)
REVERT: L   78 LEU cc_start: 0.8853 (mm) cc_final: 0.8610 (mm)
REVERT: L   79 GLU cc_start: 0.8795 (tp30) cc_final: 0.8551 (tp30)
REVERT: L  101 ASN cc_start: 0.8762 (p0) cc_final: 0.8528 (p0)
REVERT: A   83 MET cc_start: 0.8034 (tpp) cc_final: 0.7743 (mmm)
REVERT: A  125 PHE cc_start: 0.8396 (m-10) cc_final: 0.7985 (m-10)
REVERT: A  147 MET cc_start: 0.8101 (tmm) cc_final: 0.7773 (tmm)
REVERT: A  181 TYR cc_start: 0.7594 (m-80) cc_final: 0.7247 (m-10)
REVERT: A  313 LYS cc_start: 0.9331 (tppp) cc_final: 0.9091 (tppt)
REVERT: A  486 GLU cc_start: 0.8944 (tm-30) cc_final: 0.7951 (tm-30)
REVERT: A  492 MET cc_start: 0.9291 (tmm) cc_final: 0.8970 (tmm)
REVERT: A  569 GLU cc_start: 0.8857 (pm20) cc_final: 0.8593 (pm20)
REVERT: A  589 GLN cc_start: 0.8533 (pm20) cc_final: 0.8262 (pm20)
REVERT: A  609 HIS cc_start: 0.8119 (m90) cc_final: 0.7707 (m90)
REVERT: A  635 ASN cc_start: 0.8981 (p0) cc_final: 0.8701 (m-40)
REVERT: A  644 TYR cc_start: 0.8741 (m-10) cc_final: 0.8536 (m-80)
REVERT: A  647 ASP cc_start: 0.8849 (t0) cc_final: 0.8637 (t0)
REVERT: A  663 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8365 (tm-30)
REVERT: M    2 LEU cc_start: 0.8678 (pt) cc_final: 0.8390 (pp)
REVERT: M   36 TYR cc_start: 0.7055 (m-80) cc_final: 0.6149 (m-80)
REVERT: M   61 ARG cc_start: 0.7603 (ptt180) cc_final: 0.7388 (ptt180)
REVERT: M   92 PHE cc_start: 0.3965 (OUTLIER) cc_final: 0.3216 (t80)
REVERT: N   34 MET cc_start: 0.9222 (mmp) cc_final: 0.8608 (mmp)
REVERT: N   36 TRP cc_start: 0.7984 (m100) cc_final: 0.7602 (m100)
REVERT: N   50 THR cc_start: 0.9158 (t) cc_final: 0.8142 (p)
REVERT: N   62 TRP cc_start: 0.8470 (m100) cc_final: 0.8082 (m100)
REVERT: N   71 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.6957 (ttm170)
  outliers start: 44
  outliers final: 30
  residues processed: 214
  average time/residue: 0.2004
  time to fit residues: 57.4230
Evaluate side-chains
  215 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 184
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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   49 ARG
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  529 VAL
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain M residue    5 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   27 PHE
Chi-restraints excluded: chain N residue   37 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 95 optimal weight:   50.0000
   chunk 88 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 96 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0000
   chunk 56 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.150886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106000 restraints weight = 15851.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.108136 restraints weight = 8242.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.110193 restraints weight = 5352.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7938  Z= 0.185
  Angle     :  0.672   8.065  10770  Z= 0.347
  Chirality :  0.044   0.147   1220
  Planarity :  0.004   0.050   1374
  Dihedral  :  6.465  49.661   1105
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.82 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.80 (0.24), residues: 989
  helix: -1.65 (0.55), residues: 76
  sheet: -2.17 (0.32), residues: 278
  loop : -2.96 (0.21), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 300 
 HIS   0.002   0.000   HIS A 316 
 PHE   0.012   0.001   PHE A 219 
 TYR   0.012   0.001   TYR M  87 
 ARG   0.003   0.000   ARG A 361 

*********************** 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
  232 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.7950 (mp0) cc_final: 0.7488 (mp0)
REVERT: H   34 MET cc_start: 0.8861 (mmm) cc_final: 0.8281 (mmm)
REVERT: H   46 GLU cc_start: 0.6605 (tt0) cc_final: 0.6338 (tt0)
REVERT: H   79 LYS cc_start: 0.9222 (mmtp) cc_final: 0.8915 (mmtm)
REVERT: H  101 MET cc_start: 0.8722 (mmm) cc_final: 0.8439 (mtm)
REVERT: L   37 GLN cc_start: 0.9378 (tm-30) cc_final: 0.8869 (tm-30)
REVERT: L   38 GLN cc_start: 0.9019 (pp30) cc_final: 0.8494 (pm20)
REVERT: L   39 LYS cc_start: 0.8832 (tppt) cc_final: 0.8428 (tppt)
REVERT: L   42 GLN cc_start: 0.8470 (mp10) cc_final: 0.8130 (mp10)
REVERT: L   78 LEU cc_start: 0.8873 (mm) cc_final: 0.8672 (mm)
REVERT: L   79 GLU cc_start: 0.8726 (tp30) cc_final: 0.8451 (tp30)
REVERT: L  101 ASN cc_start: 0.8784 (p0) cc_final: 0.8554 (p0)
REVERT: A  125 PHE cc_start: 0.8373 (m-10) cc_final: 0.7980 (m-10)
REVERT: A  147 MET cc_start: 0.7929 (tmm) cc_final: 0.7060 (tmm)
REVERT: A  313 LYS cc_start: 0.9324 (tppp) cc_final: 0.9085 (tppt)
REVERT: A  344 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7323 (mp0)
REVERT: A  486 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: A  492 MET cc_start: 0.9332 (tmm) cc_final: 0.8998 (tmm)
REVERT: A  569 GLU cc_start: 0.8842 (pm20) cc_final: 0.8564 (pm20)
REVERT: A  609 HIS cc_start: 0.8056 (m90) cc_final: 0.7650 (m90)
REVERT: A  635 ASN cc_start: 0.8981 (p0) cc_final: 0.8665 (m-40)
REVERT: A  647 ASP cc_start: 0.8829 (t0) cc_final: 0.8619 (t0)
REVERT: A  653 ASN cc_start: 0.8916 (t0) cc_final: 0.8234 (t0)
REVERT: A  663 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8365 (tm-30)
REVERT: M    2 LEU cc_start: 0.8610 (pt) cc_final: 0.8292 (pp)
REVERT: M   36 TYR cc_start: 0.6983 (m-80) cc_final: 0.6298 (m-80)
REVERT: M   69 THR cc_start: 0.5786 (OUTLIER) cc_final: 0.5558 (m)
REVERT: M   77 ASP cc_start: 0.8566 (m-30) cc_final: 0.8210 (m-30)
REVERT: M   92 PHE cc_start: 0.3968 (OUTLIER) cc_final: 0.3283 (t80)
REVERT: M   99 ASN cc_start: 0.8923 (t0) cc_final: 0.8588 (t0)
REVERT: N   34 MET cc_start: 0.9107 (mmp) cc_final: 0.8472 (mmp)
REVERT: N   36 TRP cc_start: 0.7938 (m100) cc_final: 0.7511 (m100)
REVERT: N   50 THR cc_start: 0.9115 (t) cc_final: 0.8114 (p)
REVERT: N   71 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.6786 (ttm170)
REVERT: N  108 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7784 (m-40)
  outliers start: 33
  outliers final: 20
  residues processed: 211
  average time/residue: 0.1870
  time to fit residues: 53.4195
Evaluate side-chains
  215 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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   75 ILE
Chi-restraints excluded: chain L residue  110 VAL
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  352 HIS
Chi-restraints excluded: chain A residue  484 CYS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  603 HIS
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
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 64 optimal weight:    0.2980
   chunk 70 optimal weight:   10.0000
   chunk 92 optimal weight:    0.0010
   chunk 8 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    1.6190

-------------------------------------------------------------------------------
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
M   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.151136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.103199 restraints weight = 15728.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.106464 restraints weight = 8672.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.108636 restraints weight = 5901.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7938  Z= 0.175
  Angle     :  0.653   9.407  10770  Z= 0.337
  Chirality :  0.043   0.142   1220
  Planarity :  0.004   0.045   1374
  Dihedral  :  6.159  46.438   1105
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.63 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.89 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.24), residues: 989
  helix: -1.08 (0.58), residues: 70
  sheet: -2.03 (0.33), residues: 257
  loop : -2.84 (0.21), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP M  35 
 HIS   0.002   0.000   HIS A 316 
 PHE   0.012   0.001   PHE A 219 
 TYR   0.018   0.001   TYR M  87 
 ARG   0.002   0.000   ARG A 361 

*********************** 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
  242 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 196
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9142 (pm20)
REVERT: H    6 GLU cc_start: 0.7973 (mp0) cc_final: 0.7665 (mp0)
REVERT: H   32 TYR cc_start: 0.8765 (m-10) cc_final: 0.8524 (m-80)
REVERT: H   34 MET cc_start: 0.8873 (mmm) cc_final: 0.8549 (mmm)
REVERT: H   46 GLU cc_start: 0.6608 (tt0) cc_final: 0.6348 (tt0)
REVERT: H   79 LYS cc_start: 0.9225 (mmtp) cc_final: 0.8921 (mmtm)
REVERT: H  101 MET cc_start: 0.8737 (mmm) cc_final: 0.8439 (mtm)
REVERT: L   35 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.6443 (m-10)
REVERT: L   37 GLN cc_start: 0.9358 (tm-30) cc_final: 0.8846 (tm-30)
REVERT: L   38 GLN cc_start: 0.8977 (pp30) cc_final: 0.8492 (pm20)
REVERT: L   39 LYS cc_start: 0.8765 (tppt) cc_final: 0.8421 (tppt)
REVERT: L   42 GLN cc_start: 0.8479 (mp10) cc_final: 0.8099 (mp10)
REVERT: L   79 GLU cc_start: 0.8703 (tp30) cc_final: 0.8455 (tp30)
REVERT: L  101 ASN cc_start: 0.8751 (p0) cc_final: 0.8511 (p0)
REVERT: A   83 MET cc_start: 0.8631 (mmm) cc_final: 0.8233 (mmm)
REVERT: A  125 PHE cc_start: 0.8283 (m-10) cc_final: 0.7941 (m-10)
REVERT: A  147 MET cc_start: 0.7896 (tmm) cc_final: 0.7017 (tmm)
REVERT: A  181 TYR cc_start: 0.7541 (m-80) cc_final: 0.7183 (m-10)
REVERT: A  272 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8337 (tp30)
REVERT: A  313 LYS cc_start: 0.9332 (tppp) cc_final: 0.9068 (tppt)
REVERT: A  486 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8340 (tm-30)
REVERT: A  492 MET cc_start: 0.9261 (tmm) cc_final: 0.8911 (tmm)
REVERT: A  569 GLU cc_start: 0.8902 (pm20) cc_final: 0.8631 (pm20)
REVERT: A  609 HIS cc_start: 0.8054 (m90) cc_final: 0.7667 (m90)
REVERT: A  635 ASN cc_start: 0.8989 (p0) cc_final: 0.8691 (m-40)
REVERT: A  647 ASP cc_start: 0.8820 (t0) cc_final: 0.8584 (t0)
REVERT: A  653 ASN cc_start: 0.8915 (t0) cc_final: 0.8459 (t0)
REVERT: A  663 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8422 (tm-30)
REVERT: M    2 LEU cc_start: 0.8541 (pt) cc_final: 0.8241 (pp)
REVERT: M   36 TYR cc_start: 0.7006 (m-80) cc_final: 0.6258 (m-80)
REVERT: M   42 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7647 (tp-100)
REVERT: M   69 THR cc_start: 0.5898 (OUTLIER) cc_final: 0.5648 (m)
REVERT: M   77 ASP cc_start: 0.8561 (m-30) cc_final: 0.8355 (m-30)
REVERT: M   92 PHE cc_start: 0.4178 (OUTLIER) cc_final: 0.3529 (t80)
REVERT: M   99 ASN cc_start: 0.8963 (t0) cc_final: 0.8605 (t0)
REVERT: N   34 MET cc_start: 0.9010 (mmp) cc_final: 0.8448 (mmp)
REVERT: N   36 TRP cc_start: 0.7730 (m100) cc_final: 0.7353 (m100)
REVERT: N   50 THR cc_start: 0.9013 (t) cc_final: 0.7954 (p)
REVERT: N   71 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.6824 (ttm170)
REVERT: N  108 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7775 (m-40)
  outliers start: 46
  outliers final: 33
  residues processed: 216
  average time/residue: 0.1885
  time to fit residues: 54.8801
Evaluate side-chains
  230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   45 LEU
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   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  209 THR
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  374 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  505 VAL
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  634 GLU
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 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 13 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0000
   chunk 75 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    2.9590

-------------------------------------------------------------------------------
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
N   2 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.099890 restraints weight = 16612.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.102731 restraints weight = 9704.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104301 restraints weight = 5874.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7938  Z= 0.256
  Angle     :  0.691   8.769  10770  Z= 0.358
  Chirality :  0.045   0.158   1220
  Planarity :  0.004   0.047   1374
  Dihedral  :  6.346  47.151   1105
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.04 %
    Favored  : 86.96 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 22.70 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.25), residues: 989
  helix: -1.08 (0.56), residues: 76
  sheet: -2.01 (0.33), residues: 262
  loop : -2.81 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP M  35 
 HIS   0.003   0.001   HIS A 610 
 PHE   0.028   0.002   PHE N  27 
 TYR   0.017   0.001   TYR M  87 
 ARG   0.002   0.000   ARG A 361 

*********************** 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
  244 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 195
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8032 (mp0) cc_final: 0.7630 (mp0)
REVERT: H   32 TYR cc_start: 0.9007 (m-10) cc_final: 0.8651 (m-80)
REVERT: H   34 MET cc_start: 0.8860 (mmm) cc_final: 0.8353 (mmm)
REVERT: H   46 GLU cc_start: 0.6754 (tt0) cc_final: 0.6432 (tt0)
REVERT: L   35 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.6531 (m-10)
REVERT: L   37 GLN cc_start: 0.9380 (tm-30) cc_final: 0.9107 (tm-30)
REVERT: L   38 GLN cc_start: 0.9042 (pp30) cc_final: 0.8432 (pm20)
REVERT: L   39 LYS cc_start: 0.8826 (tppt) cc_final: 0.8468 (tppt)
REVERT: L   42 GLN cc_start: 0.8416 (mp10) cc_final: 0.8006 (mp10)
REVERT: A   83 MET cc_start: 0.8620 (mmm) cc_final: 0.8150 (mmm)
REVERT: A  125 PHE cc_start: 0.8437 (m-10) cc_final: 0.8081 (m-10)
REVERT: A  147 MET cc_start: 0.7718 (tmm) cc_final: 0.6850 (tmm)
REVERT: A  181 TYR cc_start: 0.7456 (m-80) cc_final: 0.7061 (m-10)
REVERT: A  313 LYS cc_start: 0.9326 (tppp) cc_final: 0.9050 (tppt)
REVERT: A  486 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: A  492 MET cc_start: 0.9332 (tmm) cc_final: 0.9016 (tmm)
REVERT: A  569 GLU cc_start: 0.8882 (pm20) cc_final: 0.8641 (pm20)
REVERT: A  609 HIS cc_start: 0.8129 (m90) cc_final: 0.7754 (m90)
REVERT: A  635 ASN cc_start: 0.8956 (p0) cc_final: 0.8710 (m-40)
REVERT: A  647 ASP cc_start: 0.8820 (t0) cc_final: 0.8581 (t0)
REVERT: A  653 ASN cc_start: 0.8950 (t0) cc_final: 0.8298 (t0)
REVERT: A  663 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8468 (tm-30)
REVERT: M    2 LEU cc_start: 0.8572 (pt) cc_final: 0.8249 (pp)
REVERT: M   36 TYR cc_start: 0.7118 (m-80) cc_final: 0.6339 (m-80)
REVERT: M   69 THR cc_start: 0.5819 (OUTLIER) cc_final: 0.5554 (m)
REVERT: M   92 PHE cc_start: 0.3964 (OUTLIER) cc_final: 0.3704 (t80)
REVERT: M   99 ASN cc_start: 0.9050 (t0) cc_final: 0.8780 (t0)
REVERT: N    2 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6599 (pt0)
REVERT: N   34 MET cc_start: 0.9079 (mmp) cc_final: 0.8783 (mmp)
REVERT: N   36 TRP cc_start: 0.7681 (m100) cc_final: 0.7305 (m100)
REVERT: N   68 THR cc_start: 0.8841 (m) cc_final: 0.8480 (p)
REVERT: N   71 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6871 (ttm170)
REVERT: N  108 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7980 (m-40)
  outliers start: 49
  outliers final: 36
  residues processed: 217
  average time/residue: 0.2930
  time to fit residues: 86.0122
Evaluate side-chains
  230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 189
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   46 PHE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   84 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  258 LYS
Chi-restraints excluded: chain A residue  283 THR
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  505 VAL
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  613 THR
Chi-restraints excluded: chain A residue  627 SER
Chi-restraints excluded: chain A residue  634 GLU
Chi-restraints excluded: chain A residue  657 LEU
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    2 GLN
Chi-restraints excluded: chain N residue    4 VAL
Chi-restraints excluded: chain N residue   19 THR
Chi-restraints excluded: chain N residue   45 LEU
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   79 LYS
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 40 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0010
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.9588

-------------------------------------------------------------------------------
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   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.151718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.105008 restraints weight = 16494.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107818 restraints weight = 9338.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.110112 restraints weight = 5607.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7938  Z= 0.152
  Angle     :  0.657   9.849  10770  Z= 0.335
  Chirality :  0.044   0.150   1220
  Planarity :  0.004   0.048   1374
  Dihedral  :  5.906  47.275   1105
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.92 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 24.10 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.25), residues: 989
  helix: -0.55 (0.60), residues: 72
  sheet: -1.89 (0.33), residues: 257
  loop : -2.65 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP N  47 
 HIS   0.001   0.000   HIS A 316 
 PHE   0.009   0.001   PHE N  92 
 TYR   0.016   0.001   TYR M  87 
 ARG   0.002   0.000   ARG A 361 

*********************** 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
  240 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 199
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.7944 (mp0) cc_final: 0.7436 (mp0)
REVERT: H   34 MET cc_start: 0.8969 (mmm) cc_final: 0.8721 (mmm)
REVERT: H   79 LYS cc_start: 0.9142 (mmtp) cc_final: 0.8831 (mmtm)
REVERT: H  101 MET cc_start: 0.8243 (mtt) cc_final: 0.7901 (mtm)
REVERT: L   35 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.6403 (m-10)
REVERT: L   37 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8826 (tm-30)
REVERT: L   38 GLN cc_start: 0.8860 (pp30) cc_final: 0.8613 (pm20)
REVERT: L   39 LYS cc_start: 0.8724 (tppt) cc_final: 0.8501 (tppt)
REVERT: L   42 GLN cc_start: 0.8472 (mp10) cc_final: 0.8128 (mp10)
REVERT: A   83 MET cc_start: 0.8461 (mmm) cc_final: 0.8086 (mmm)
REVERT: A  147 MET cc_start: 0.7668 (tmm) cc_final: 0.6766 (tmm)
REVERT: A  231 GLU cc_start: 0.8532 (mp0) cc_final: 0.8312 (mp0)
REVERT: A  232 MET cc_start: 0.8318 (ptm) cc_final: 0.8043 (ptt)
REVERT: A  313 LYS cc_start: 0.9322 (tppp) cc_final: 0.9028 (tppt)
REVERT: A  344 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7555 (mp0)
REVERT: A  486 GLU cc_start: 0.8864 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: A  492 MET cc_start: 0.9254 (tmm) cc_final: 0.8944 (tmm)
REVERT: A  569 GLU cc_start: 0.8937 (pm20) cc_final: 0.8670 (pm20)
REVERT: A  609 HIS cc_start: 0.8117 (m90) cc_final: 0.7750 (m90)
REVERT: A  635 ASN cc_start: 0.8919 (p0) cc_final: 0.8708 (m-40)
REVERT: A  647 ASP cc_start: 0.8747 (t0) cc_final: 0.8517 (t0)
REVERT: A  653 ASN cc_start: 0.8911 (t0) cc_final: 0.8464 (t0)
REVERT: A  663 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8465 (tm-30)
REVERT: M   36 TYR cc_start: 0.7061 (m-80) cc_final: 0.6355 (m-80)
REVERT: M   42 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7520 (tp-100)
REVERT: M   69 THR cc_start: 0.5754 (OUTLIER) cc_final: 0.5490 (m)
REVERT: M   99 ASN cc_start: 0.9042 (t0) cc_final: 0.8602 (t0)
REVERT: N   34 MET cc_start: 0.8800 (mmp) cc_final: 0.8473 (mmp)
REVERT: N   36 TRP cc_start: 0.7489 (m100) cc_final: 0.7112 (m100)
REVERT: N   71 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.6949 (ttm170)
REVERT: N   95 ARG cc_start: 0.6161 (tmm-80) cc_final: 0.5850 (tmm-80)
REVERT: N  108 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7652 (m-40)
  outliers start: 41
  outliers final: 28
  residues processed: 218
  average time/residue: 0.1955
  time to fit residues: 57.2635
Evaluate side-chains
  225 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 194
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   75 ILE
Chi-restraints excluded: chain L residue  108 LYS
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  209 THR
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  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 M residue   69 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 93 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 60 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.151440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111319 restraints weight = 16501.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.110756 restraints weight = 8003.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.111330 restraints weight = 7907.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7938  Z= 0.174
  Angle     :  0.691  10.577  10770  Z= 0.348
  Chirality :  0.044   0.173   1220
  Planarity :  0.004   0.042   1374
  Dihedral  :  5.645  47.601   1103
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 25.73 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.25), residues: 989
  helix: -0.28 (0.61), residues: 72
  sheet: -1.71 (0.34), residues: 241
  loop : -2.65 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP M  35 
 HIS   0.002   0.000   HIS A 316 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.014   0.001   TYR H  32 
 ARG   0.002   0.000   ARG A 361 

*********************** 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
  232 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.7884 (mp0) cc_final: 0.7451 (mp0)
REVERT: H   34 MET cc_start: 0.8929 (mmm) cc_final: 0.8667 (mmm)
REVERT: H   46 GLU cc_start: 0.6346 (tt0) cc_final: 0.5873 (tt0)
REVERT: H   47 TYR cc_start: 0.8080 (t80) cc_final: 0.7682 (t80)
REVERT: L   35 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.6524 (m-10)
REVERT: L   37 GLN cc_start: 0.9400 (tm-30) cc_final: 0.8838 (tm-30)
REVERT: L   39 LYS cc_start: 0.8785 (tppt) cc_final: 0.8373 (tppt)
REVERT: L   42 GLN cc_start: 0.8385 (mp10) cc_final: 0.7980 (mp10)
REVERT: A   83 MET cc_start: 0.7996 (mmm) cc_final: 0.7546 (mmm)
REVERT: A  147 MET cc_start: 0.7898 (tmm) cc_final: 0.6984 (tmm)
REVERT: A  181 TYR cc_start: 0.7347 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  304 ASP cc_start: 0.8196 (t0) cc_final: 0.7961 (t0)
REVERT: A  313 LYS cc_start: 0.9340 (tppp) cc_final: 0.9066 (tppt)
REVERT: A  344 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7562 (mp0)
REVERT: A  486 GLU cc_start: 0.8864 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: A  492 MET cc_start: 0.9248 (tmm) cc_final: 0.8896 (tmm)
REVERT: A  501 ASN cc_start: 0.8862 (p0) cc_final: 0.8106 (p0)
REVERT: A  569 GLU cc_start: 0.8937 (pm20) cc_final: 0.8680 (pm20)
REVERT: A  609 HIS cc_start: 0.8172 (m90) cc_final: 0.7806 (m90)
REVERT: A  635 ASN cc_start: 0.8944 (p0) cc_final: 0.8710 (m-40)
REVERT: A  647 ASP cc_start: 0.8756 (t0) cc_final: 0.8524 (t0)
REVERT: A  653 ASN cc_start: 0.8941 (t0) cc_final: 0.8505 (t0)
REVERT: A  663 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8655 (tm-30)
REVERT: M   36 TYR cc_start: 0.7036 (m-80) cc_final: 0.6340 (m-80)
REVERT: M   69 THR cc_start: 0.5961 (OUTLIER) cc_final: 0.5692 (m)
REVERT: N   27 PHE cc_start: 0.7241 (p90) cc_final: 0.6094 (p90)
REVERT: N   36 TRP cc_start: 0.7463 (m100) cc_final: 0.7161 (m100)
REVERT: N   71 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7180 (ttm170)
REVERT: N  108 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7512 (m-40)
  outliers start: 35
  outliers final: 27
  residues processed: 210
  average time/residue: 0.1969
  time to fit residues: 55.4545
Evaluate side-chains
  222 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   75 ILE
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  209 THR
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  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 M residue   69 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.152353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.103558 restraints weight = 16734.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.107267 restraints weight = 8324.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109664 restraints weight = 5424.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7938  Z= 0.193
  Angle     :  0.694  11.175  10770  Z= 0.352
  Chirality :  0.044   0.151   1220
  Planarity :  0.004   0.041   1374
  Dihedral  :  5.706  48.809   1103
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.32 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 24.68 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.25), residues: 989
  helix: -0.20 (0.62), residues: 72
  sheet: -1.74 (0.34), residues: 248
  loop : -2.61 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP M  35 
 HIS   0.002   0.000   HIS A 316 
 PHE   0.011   0.001   PHE A 219 
 TYR   0.019   0.001   TYR M  87 
 ARG   0.002   0.000   ARG A 361 

*********************** 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
  234 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 196
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.7782 (mp0) cc_final: 0.7146 (mp0)
REVERT: H   34 MET cc_start: 0.8804 (mmm) cc_final: 0.8510 (mmm)
REVERT: H   46 GLU cc_start: 0.6412 (tt0) cc_final: 0.5955 (tt0)
REVERT: H   47 TYR cc_start: 0.7952 (t80) cc_final: 0.7602 (t80)
REVERT: H  101 MET cc_start: 0.8379 (mtm) cc_final: 0.8105 (mtp)
REVERT: L   35 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.6591 (m-10)
REVERT: L   37 GLN cc_start: 0.9409 (tm-30) cc_final: 0.8878 (tm-30)
REVERT: L   39 LYS cc_start: 0.8901 (tppt) cc_final: 0.8433 (tppt)
REVERT: L   42 GLN cc_start: 0.8414 (mp10) cc_final: 0.8033 (mp10)
REVERT: L  100 PHE cc_start: 0.8983 (m-80) cc_final: 0.8613 (m-80)
REVERT: A   83 MET cc_start: 0.8627 (mmm) cc_final: 0.8337 (mmm)
REVERT: A  147 MET cc_start: 0.7869 (tmm) cc_final: 0.6964 (tmm)
REVERT: A  181 TYR cc_start: 0.7287 (m-80) cc_final: 0.7052 (m-80)
REVERT: A  313 LYS cc_start: 0.9268 (tppp) cc_final: 0.9065 (tppt)
REVERT: A  344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7550 (mp0)
REVERT: A  486 GLU cc_start: 0.8831 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: A  492 MET cc_start: 0.9258 (tmm) cc_final: 0.8915 (tmm)
REVERT: A  550 MET cc_start: 0.8938 (mpp) cc_final: 0.8691 (mpp)
REVERT: A  569 GLU cc_start: 0.8879 (pm20) cc_final: 0.8661 (pm20)
REVERT: A  582 LYS cc_start: 0.8846 (tptt) cc_final: 0.8489 (tptp)
REVERT: A  609 HIS cc_start: 0.8160 (m90) cc_final: 0.7751 (m90)
REVERT: A  647 ASP cc_start: 0.8726 (t0) cc_final: 0.8493 (t0)
REVERT: A  653 ASN cc_start: 0.8952 (t0) cc_final: 0.8318 (t0)
REVERT: A  663 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8454 (tm-30)
REVERT: M   22 LYS cc_start: 0.8145 (pttp) cc_final: 0.7863 (ptpp)
REVERT: M   36 TYR cc_start: 0.6970 (m-80) cc_final: 0.6289 (m-80)
REVERT: M   69 THR cc_start: 0.5862 (OUTLIER) cc_final: 0.5493 (m)
REVERT: N   27 PHE cc_start: 0.7259 (p90) cc_final: 0.6022 (p90)
REVERT: N   36 TRP cc_start: 0.7470 (m100) cc_final: 0.7195 (m100)
REVERT: N   71 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7193 (ttm170)
  outliers start: 38
  outliers final: 34
  residues processed: 211
  average time/residue: 0.2041
  time to fit residues: 57.7169
Evaluate side-chains
  230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   75 ILE
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   49 ARG
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  209 THR
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  315 ILE
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  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  634 GLU
Chi-restraints excluded: chain M residue   69 THR
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   79 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:   30.0000
   chunk 59 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN
A  77 HIS
A 533 GLN
A 669 GLN
M   6 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.145976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096793 restraints weight = 16837.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.100157 restraints weight = 8910.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.102351 restraints weight = 5992.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7938  Z= 0.326
  Angle     :  0.780  11.311  10770  Z= 0.398
  Chirality :  0.046   0.162   1220
  Planarity :  0.004   0.041   1374
  Dihedral  :  6.352  51.347   1103
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.65 %
    Favored  : 86.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.25), residues: 989
  helix: -0.78 (0.60), residues: 70
  sheet: -1.94 (0.32), residues: 260
  loop : -2.68 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP M  35 
 HIS   0.005   0.001   HIS A 610 
 PHE   0.018   0.002   PHE A 219 
 TYR   0.020   0.002   TYR M  87 
 ARG   0.003   0.000   ARG H  38 

********************** 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
  239 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.7998 (mp0) cc_final: 0.7624 (mp0)
REVERT: H   34 MET cc_start: 0.8753 (mmm) cc_final: 0.8318 (mmm)
REVERT: H   46 GLU cc_start: 0.6316 (tt0) cc_final: 0.5844 (tt0)
REVERT: H   47 TYR cc_start: 0.8063 (t80) cc_final: 0.7685 (t80)
REVERT: H   79 LYS cc_start: 0.9208 (mmtp) cc_final: 0.8877 (mmtm)
REVERT: H  101 MET cc_start: 0.8351 (mtm) cc_final: 0.8100 (mtp)
REVERT: L   35 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.6369 (m-10)
REVERT: L   37 GLN cc_start: 0.9405 (tm-30) cc_final: 0.8913 (tm-30)
REVERT: L   38 GLN cc_start: 0.9039 (pp30) cc_final: 0.8419 (pm20)
REVERT: L   42 GLN cc_start: 0.8426 (mp10) cc_final: 0.8123 (mp10)
REVERT: L   46 LEU cc_start: 0.8308 (pt) cc_final: 0.8099 (pt)
REVERT: L   79 GLU cc_start: 0.8527 (tp30) cc_final: 0.8149 (tp30)
REVERT: A   83 MET cc_start: 0.8761 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  147 MET cc_start: 0.7681 (tmm) cc_final: 0.6794 (tmm)
REVERT: A  181 TYR cc_start: 0.7407 (m-80) cc_final: 0.7157 (m-80)
REVERT: A  313 LYS cc_start: 0.9365 (tppp) cc_final: 0.9083 (tppt)
REVERT: A  356 GLU cc_start: 0.9070 (tp30) cc_final: 0.8845 (mm-30)
REVERT: A  486 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: A  492 MET cc_start: 0.9306 (tmm) cc_final: 0.9003 (tmm)
REVERT: A  550 MET cc_start: 0.8996 (mpp) cc_final: 0.8743 (mpp)
REVERT: A  569 GLU cc_start: 0.8935 (pm20) cc_final: 0.8727 (pm20)
REVERT: A  609 HIS cc_start: 0.8186 (m90) cc_final: 0.7844 (m90)
REVERT: A  647 ASP cc_start: 0.8845 (t0) cc_final: 0.8603 (t0)
REVERT: A  653 ASN cc_start: 0.8977 (t0) cc_final: 0.8454 (t0)
REVERT: A  663 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8503 (tm-30)
REVERT: M   69 THR cc_start: 0.5757 (OUTLIER) cc_final: 0.5494 (m)
REVERT: N   50 THR cc_start: 0.9013 (t) cc_final: 0.7855 (p)
REVERT: N   62 TRP cc_start: 0.7805 (m-10) cc_final: 0.7143 (p-90)
REVERT: N   71 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.6837 (ttm170)
  outliers start: 45
  outliers final: 38
  residues processed: 214
  average time/residue: 0.1948
  time to fit residues: 56.5915
Evaluate side-chains
  230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
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   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  108 LYS
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   49 ARG
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  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  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  657 LEU
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue    6 GLN
Chi-restraints excluded: chain M residue   69 THR
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   79 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0270
   chunk 51 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 92 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.0644

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

Flipped N/Q/H residues before XYZ refinement:
H 100 ASN
** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3884 r_free = 0.3884 target = 0.146070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.099071 restraints weight = 16733.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.101949 restraints weight = 9577.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.103720 restraints weight = 5798.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.329   7938  Z= 0.513
  Angle     :  1.095  59.196  10770  Z= 0.617
  Chirality :  0.048   0.519   1220
  Planarity :  0.005   0.071   1374
  Dihedral  :  6.396  51.425   1103
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.85 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 23.86 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.25), residues: 989
  helix: -0.78 (0.60), residues: 70
  sheet: -1.96 (0.32), residues: 260
  loop : -2.69 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.007   TRP N  36 
 HIS   0.004   0.001   HIS A 610 
 PHE   0.018   0.001   PHE A 219 
 TYR   0.086   0.002   TYR A 282 
 ARG   0.008   0.000   ARG M  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3056.20 seconds
wall clock time: 54 minutes 45.86 seconds (3285.86 seconds total)