Starting phenix.real_space_refine
on Fri Aug 22 17:45:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gau_29908/08_2025/8gau_29908.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gau_29908/08_2025/8gau_29908.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gau_29908/08_2025/8gau_29908.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gau_29908/08_2025/8gau_29908.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gau_29908/08_2025/8gau_29908.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gau_29908/08_2025/8gau_29908.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.035
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      34      5.16       5
     C    4163      2.51       5
     N    1133      2.21       5
     O    1274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6604
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 2987
          Classifications: {'peptide': 386}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 372}
    Chain: "H"
      Number of atoms: 974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 974
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 7, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 798
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
    Chain: "M"
      Number of atoms: 998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 998
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 6, 'TRANS': 120}
    Chain: "N"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 833
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.35, per 1000 atoms: 0.20
  Number of scatterers: 6604
  At special positions: 0
  Unit cell: (105.45, 93.24, 113.22, 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      34     16.00
     O    1274      8.00
     N    1133      7.00
     C    4163      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS A 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 124 " - pdb=" SG  CYS A 129 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 175 " - pdb=" SG  CYS A 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 183 " - pdb=" SG  CYS A 230 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 289 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 318 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 421 " - pdb=" SG  CYS A 447 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A 200 "
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 411.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1530

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 20 sheets defined
      2.9% alpha, 33.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.674A  pdb=" N   SER A 145 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASN A 146 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 146'
    Processing helix  chain 'H' and resid 99 through 100C
      removed outlier: 3.757A  pdb=" N   VAL H 100B" --> pdb=" O   TYR H  99 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   HIS H 100C" --> pdb=" O   ASP H 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 99 through 100C'
    Processing helix  chain 'M' and resid 28 through 32
      removed outlier: 3.717A  pdb=" N   ASP M  31 " --> pdb=" O   LYS M  28 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR M  32 " --> pdb=" O   PHE M  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 28 through 32'
    Processing helix  chain 'M' and resid 61 through 64
      removed outlier: 3.715A  pdb=" N   LYS M  64 " --> pdb=" O   ASP M  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 61 through 64'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102
      removed outlier: 6.828A  pdb=" N   VAL A 445 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   LYS A 102 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 443 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ARG A 420 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 121
      removed outlier: 5.372A  pdb=" N   GLU A 119 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU A 134 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ALA A 133 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184
      removed outlier: 3.659A  pdb=" N   SER A 179 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ALA A 203 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   SER A 214 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE A 205 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233
      removed outlier: 3.969A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   HIS A 264 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   GLU A 258 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ILE A 262 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 283
      removed outlier: 3.715A  pdb=" N   SER A 311 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356
      removed outlier: 4.834A  pdb=" N   TRP A 352 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLY A 363 " --> pdb=" O   TRP A 352 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASP A 356 " --> pdb=" O   ASP A 359 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASP A 359 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET A 362 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE A 377 " --> pdb=" O   MET A 362 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   LEU A 372 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   GLU A 399 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   TYR A 374 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   LYS A 378 " --> pdb=" O   ASN A 393 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   ASN A 393 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 22
      removed outlier: 3.542A  pdb=" N   SER H  79 " --> pdb=" O   SER H  70 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER H  70 " --> pdb=" O   SER H  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 59
      removed outlier: 3.505A  pdb=" N   GLU H  50 " --> pdb=" O   THR H  58 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.827A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 34 through 37
      removed outlier: 3.802A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 62 through 63
    Processing sheet with id=AB4, first strand: chain 'L' and resid 66 through 67
      removed outlier: 3.853A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 5
      removed outlier: 3.762A  pdb=" N   GLN M   3 " --> pdb=" O   SER M  25 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER M  25 " --> pdb=" O   GLN M   3 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'M' and resid 18 through 21
      removed outlier: 3.645A  pdb=" N   LEU M  18 " --> pdb=" O   ILE M  82 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE M  82 " --> pdb=" O   LEU M  18 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU M  80 " --> pdb=" O   LEU M  20 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR M  79 " --> pdb=" O   SER M  70 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER M  70 " --> pdb=" O   TYR M  79 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'M' and resid 57 through 59
      removed outlier: 6.890A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   GLY M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   MET M  34 " --> pdb=" O   GLY M  50 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU M  89 " --> pdb=" O   GLN M  39 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   CYS M  92 " --> pdb=" O   TRP M 103 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   TRP M 103 " --> pdb=" O   CYS M  92 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ARG M  94 " --> pdb=" O   ASP M 101 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'M' and resid 57 through 59
      removed outlier: 6.890A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   GLY M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   MET M  34 " --> pdb=" O   GLY M  50 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU M  89 " --> pdb=" O   GLN M  39 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7
      removed outlier: 3.592A  pdb=" N   SER N  63 " --> pdb=" O   THR N  74 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13
      removed outlier: 3.599A  pdb=" N   ASP N 105 " --> pdb=" O   LEU N  11 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'N' and resid 53 through 54
      removed outlier: 6.694A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR N  87 " --> pdb=" O   TYR N  36 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN N  38 " --> pdb=" O   THR N  85 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR N  85 " --> pdb=" O   GLN N  38 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    423 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: 0.82

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1971
        1.33 -     1.46: 1709
        1.46 -     1.58: 3047
        1.58 -     1.71: 0
        1.71 -     1.83: 42
  Bond restraints: 6769
  Sorted by residual:
  bond pdb=" N   CYS A 183 "
       pdb=" CA  CYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.040 1.32e-02 5.74e+03 8.98e+00
  bond pdb=" N   HIS A 184 "
       pdb=" CA  HIS A 184 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.23e-02 6.61e+03 7.49e+00
  bond pdb=" N   ARG A 327 "
       pdb=" CA  ARG A 327 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.16e-02 7.43e+03 7.40e+00
  bond pdb=" N   ASN A 367 "
       pdb=" CA  ASN A 367 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 7.28e+00
  bond pdb=" N   ASP A 359 "
       pdb=" CA  ASP A 359 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.036 1.36e-02 5.41e+03 6.93e+00
  ... (remaining 6764 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 8703
        2.13 -     4.27: 418
        4.27 -     6.40: 59
        6.40 -     8.53: 14
        8.53 -    10.67: 3
  Bond angle restraints: 9197
  Sorted by residual:
  angle pdb=" CA  PHE H  31 "
        pdb=" C   PHE H  31 "
        pdb=" O   PHE H  31 "
      ideal   model   delta    sigma   weight residual
     120.43  113.36    7.07 1.12e+00 7.97e-01 3.99e+01
  angle pdb=" N   ARG H  66 "
        pdb=" CA  ARG H  66 "
        pdb=" C   ARG H  66 "
      ideal   model   delta    sigma   weight residual
     114.39  105.95    8.44 1.45e+00 4.76e-01 3.39e+01
  angle pdb=" C   PRO A 326 "
        pdb=" CA  PRO A 326 "
        pdb=" CB  PRO A 326 "
      ideal   model   delta    sigma   weight residual
     111.40  116.04   -4.64 9.10e-01 1.21e+00 2.60e+01
  angle pdb=" CA  ARG A 430 "
        pdb=" C   ARG A 430 "
        pdb=" O   ARG A 430 "
      ideal   model   delta    sigma   weight residual
     122.01  116.67    5.34 1.05e+00 9.07e-01 2.58e+01
  angle pdb=" C   VAL H 100B"
        pdb=" N   HIS H 100C"
        pdb=" CA  HIS H 100C"
      ideal   model   delta    sigma   weight residual
     120.54  127.19   -6.65 1.35e+00 5.49e-01 2.42e+01
  ... (remaining 9192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 3746
       14.99 -    29.99: 170
       29.99 -    44.98: 58
       44.98 -    59.97: 16
       59.97 -    74.96: 5
  Dihedral angle restraints: 3995
    sinusoidal: 1579
      harmonic: 2416
  Sorted by residual:
  dihedral pdb=" CA  ARG M  13 "
           pdb=" C   ARG M  13 "
           pdb=" N   PRO M  14 "
           pdb=" CA  PRO M  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.43  -34.57     0      5.00e+00 4.00e-02 4.78e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.36  -59.36     1      1.00e+01 1.00e-02 4.71e+01
  dihedral pdb=" CD  ARG A 430 "
           pdb=" NE  ARG A 430 "
           pdb=" CZ  ARG A 430 "
           pdb=" NH1 ARG A 430 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -58.81   58.81     1      1.00e+01 1.00e-02 4.63e+01
  ... (remaining 3992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 752
       0.064 -    0.129: 200
       0.129 -    0.193: 42
       0.193 -    0.257: 2
       0.257 -    0.322: 1
  Chirality restraints: 997
  Sorted by residual:
  chirality pdb=" CA  PHE H  33 "
            pdb=" N   PHE H  33 "
            pdb=" C   PHE H  33 "
            pdb=" CB  PHE H  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CB  ILE H  60 "
            pdb=" CA  ILE H  60 "
            pdb=" CG1 ILE H  60 "
            pdb=" CG2 ILE H  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  PHE H  31 "
            pdb=" N   PHE H  31 "
            pdb=" C   PHE H  31 "
            pdb=" CB  PHE H  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 994 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 430 "   -0.933 9.50e-02 1.11e+02   4.18e-01 1.06e+02
        pdb=" NE  ARG A 430 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 430 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 430 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 430 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 327 "   -0.321 9.50e-02 1.11e+02   1.44e-01 1.27e+01
        pdb=" NE  ARG A 327 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 327 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 327 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 327 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H  28 "   -0.015 2.00e-02 2.50e+03   2.96e-02 8.78e+00
        pdb=" C   SER H  28 "    0.051 2.00e-02 2.50e+03
        pdb=" O   SER H  28 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PHE H  29 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1820
        2.81 -     3.33: 5138
        3.33 -     3.85: 10435
        3.85 -     4.38: 11342
        4.38 -     4.90: 20836
  Nonbonded interactions: 49571
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 217 "
            pdb=" OD2 ASP A 243 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OE1 GLN A 136 "
            pdb=" NH1 ARG A 156 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OE2 GLU A 277 "
            pdb=" OH  TYR M 100A"
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER M  17 "
            pdb=" OD1 ASN M  82A"
     model   vdw
     2.353 3.040
  nonbonded pdb=" OH  TYR H  32 "
            pdb=" O   PRO H 100H"
     model   vdw
     2.365 3.040
  ... (remaining 49566 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:             1.000
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   6783  Z= 0.324
  Angle     :  1.056  12.196   9226  Z= 0.610
  Chirality :  0.061   0.322    997
  Planarity :  0.015   0.418   1179
  Dihedral  : 10.366  74.963   2426
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 10.11 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  3.17 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.38 (0.24), residues: 841
  helix: -4.72 (0.38), residues: 6
  sheet: -2.42 (0.25), residues: 346
  loop : -3.37 (0.22), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 156 
 TYR   0.036   0.003   TYR M  32 
 PHE   0.028   0.003   PHE H  78 
 TRP   0.039   0.004   TRP M 103 
 HIS   0.004   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 6769)
  covalent geometry    : angle       1.04374 ( 9197)
  SS BOND              : bond        0.00979 (   13)
  SS BOND              : angle       2.94023 (   26)
  hydrogen bonds       : bond        0.27695 (  151)
  hydrogen bonds       : angle      10.22531 (  423)
  link_NAG-ASN         : bond        0.00772 (    1)
  link_NAG-ASN         : angle       4.22272 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 301
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8254 (mttt) cc_final: 0.7832 (mmtt)
REVERT: A  104 ASN cc_start: 0.8403 (m-40) cc_final: 0.8122 (m110)
REVERT: A  105 SER cc_start: 0.8372 (t) cc_final: 0.8013 (m)
REVERT: A  108 LEU cc_start: 0.8325 (mt) cc_final: 0.8119 (mt)
REVERT: A  119 GLU cc_start: 0.7292 (mp0) cc_final: 0.6889 (mp0)
REVERT: A  128 LYS cc_start: 0.8011 (pttm) cc_final: 0.7345 (pttm)
REVERT: A  134 LEU cc_start: 0.8389 (mt) cc_final: 0.8102 (mp)
REVERT: A  142 ASN cc_start: 0.8227 (t0) cc_final: 0.7845 (t0)
REVERT: A  162 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7277 (mt-10)
REVERT: A  187 LYS cc_start: 0.8594 (mttt) cc_final: 0.8369 (mtmm)
REVERT: A  206 ILE cc_start: 0.8664 (mt) cc_final: 0.8447 (mm)
REVERT: A  229 GLU cc_start: 0.7510 (pt0) cc_final: 0.7300 (pt0)
REVERT: A  233 ILE cc_start: 0.8602 (mt) cc_final: 0.8250 (mm)
REVERT: A  236 THR cc_start: 0.8361 (m) cc_final: 0.8020 (p)
REVERT: A  251 ASP cc_start: 0.7459 (m-30) cc_final: 0.7119 (m-30)
REVERT: A  258 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6684 (mt-10)
REVERT: A  265 ILE cc_start: 0.8888 (mt) cc_final: 0.8684 (mm)
REVERT: A  302 ILE cc_start: 0.8671 (mt) cc_final: 0.8109 (mm)
REVERT: A  307 VAL cc_start: 0.8665 (m) cc_final: 0.8397 (t)
REVERT: A  309 ASN cc_start: 0.7478 (p0) cc_final: 0.7223 (t0)
REVERT: A  319 SER cc_start: 0.8539 (t) cc_final: 0.8293 (p)
REVERT: A  328 LYS cc_start: 0.8118 (mttt) cc_final: 0.7640 (mttt)
REVERT: A  343 GLU cc_start: 0.7239 (mp0) cc_final: 0.6948 (mp0)
REVERT: A  370 LEU cc_start: 0.8673 (mt) cc_final: 0.8471 (mm)
REVERT: A  375 GLU cc_start: 0.7634 (pt0) cc_final: 0.7152 (pt0)
REVERT: A  378 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7860 (ttpp)
REVERT: A  380 ILE cc_start: 0.8127 (mt) cc_final: 0.7917 (mm)
REVERT: A  385 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8066 (mtpp)
REVERT: A  413 GLU cc_start: 0.7438 (tt0) cc_final: 0.7136 (tt0)
REVERT: A  416 SER cc_start: 0.8892 (m) cc_final: 0.8404 (p)
REVERT: A  427 ILE cc_start: 0.8161 (mt) cc_final: 0.7732 (tp)
REVERT: A  433 GLU cc_start: 0.7590 (mp0) cc_final: 0.6784 (mp0)
REVERT: A  437 TRP cc_start: 0.8286 (m100) cc_final: 0.7699 (m-10)
REVERT: A  440 SER cc_start: 0.8643 (t) cc_final: 0.8295 (p)
REVERT: A  445 VAL cc_start: 0.8368 (t) cc_final: 0.8030 (p)
REVERT: H   13 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7362 (mtmm)
REVERT: H   16 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7438 (mt-10)
REVERT: H   22 CYS cc_start: 0.6132 (t) cc_final: 0.5751 (t)
REVERT: H   29 PHE cc_start: 0.7984 (t80) cc_final: 0.7627 (t80)
REVERT: H   31 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7291 (p90)
REVERT: H   60 ILE cc_start: 0.8172 (tp) cc_final: 0.7958 (tp)
REVERT: H  100 HIS cc_start: 0.7566 (t-90) cc_final: 0.7196 (t-90)
REVERT: H  100 LEU cc_start: 0.8159 (mt) cc_final: 0.7784 (mt)
REVERT: L    7 SER cc_start: 0.8699 (m) cc_final: 0.8351 (p)
REVERT: L   58 VAL cc_start: 0.8839 (t) cc_final: 0.8540 (p)
REVERT: L  103 LYS cc_start: 0.8068 (tttt) cc_final: 0.7431 (tttt)
REVERT: L  104 VAL cc_start: 0.8152 (t) cc_final: 0.7910 (m)
REVERT: M   32 TYR cc_start: 0.7842 (m-10) cc_final: 0.7384 (m-10)
REVERT: N   26 SER cc_start: 0.8338 (p) cc_final: 0.8067 (m)
REVERT: N   82 ASP cc_start: 0.8080 (m-30) cc_final: 0.7804 (m-30)
REVERT: N   86 TYR cc_start: 0.8093 (m-10) cc_final: 0.7563 (m-80)
REVERT: N   89 GLN cc_start: 0.7883 (tm130) cc_final: 0.7529 (tm130)
REVERT: N  103 LYS cc_start: 0.7924 (tptt) cc_final: 0.7640 (tptt)
  outliers start: 7
  outliers final: 3
  residues processed: 303
  average time/residue: 0.0678
  time to fit residues: 27.3565
Evaluate side-chains
  283 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 279
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain H residue   31 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.1980
   chunk 61 optimal weight:    0.0170
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
A  93 ASN
A 273 GLN
A 347 HIS
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 105 GLN
L  89 GLN
M  81 HIS
N  89 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.107842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.095052 restraints weight = 11883.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.098366 restraints weight = 5001.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.100312 restraints weight = 2551.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.101603 restraints weight = 1511.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.102386 restraints weight = 1001.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6783  Z= 0.103
  Angle     :  0.624   7.649   9226  Z= 0.324
  Chirality :  0.046   0.155    997
  Planarity :  0.005   0.046   1179
  Dihedral  :  6.250  59.763    959
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.95 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.49 (0.26), residues: 841
  helix: -4.01 (0.58), residues: 6
  sheet: -1.57 (0.28), residues: 324
  loop : -2.94 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 292 
 TYR   0.019   0.001   TYR M 100A
 PHE   0.013   0.002   PHE A 446 
 TRP   0.018   0.001   TRP H   7 
 HIS   0.001   0.000   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6769)
  covalent geometry    : angle       0.62079 ( 9197)
  SS BOND              : bond        0.00332 (   13)
  SS BOND              : angle       0.88516 (   26)
  hydrogen bonds       : bond        0.03682 (  151)
  hydrogen bonds       : angle       6.47544 (  423)
  link_NAG-ASN         : bond        0.00107 (    1)
  link_NAG-ASN         : angle       2.75432 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 258
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8175 (mttt) cc_final: 0.7787 (mmtt)
REVERT: A  104 ASN cc_start: 0.8323 (m-40) cc_final: 0.7971 (m110)
REVERT: A  128 LYS cc_start: 0.8020 (pttm) cc_final: 0.7384 (pttm)
REVERT: A  142 ASN cc_start: 0.8024 (t0) cc_final: 0.7800 (t0)
REVERT: A  162 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7240 (mt-10)
REVERT: A  176 MET cc_start: 0.6507 (mtm) cc_final: 0.5893 (mtt)
REVERT: A  187 LYS cc_start: 0.8652 (mttt) cc_final: 0.8448 (mtmm)
REVERT: A  236 THR cc_start: 0.8301 (m) cc_final: 0.7846 (p)
REVERT: A  245 SER cc_start: 0.8508 (t) cc_final: 0.8285 (t)
REVERT: A  249 LYS cc_start: 0.8380 (mttt) cc_final: 0.7927 (mtpp)
REVERT: A  251 ASP cc_start: 0.7424 (m-30) cc_final: 0.7074 (m-30)
REVERT: A  258 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6838 (mt-10)
REVERT: A  261 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7542 (tmmm)
REVERT: A  276 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6633 (mm-30)
REVERT: A  292 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7292 (ptt180)
REVERT: A  302 ILE cc_start: 0.8525 (mt) cc_final: 0.8043 (mm)
REVERT: A  309 ASN cc_start: 0.7456 (p0) cc_final: 0.7209 (t0)
REVERT: A  327 ARG cc_start: 0.8267 (ptt-90) cc_final: 0.8042 (ptt-90)
REVERT: A  343 GLU cc_start: 0.7331 (mp0) cc_final: 0.6823 (mp0)
REVERT: A  356 ASP cc_start: 0.8165 (t0) cc_final: 0.7933 (t0)
REVERT: A  370 LEU cc_start: 0.8641 (mt) cc_final: 0.8412 (mm)
REVERT: A  375 GLU cc_start: 0.7649 (pt0) cc_final: 0.7095 (pt0)
REVERT: A  378 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7866 (ttpt)
REVERT: A  381 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6978 (mm-30)
REVERT: A  385 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7989 (mtpp)
REVERT: A  388 SER cc_start: 0.8358 (t) cc_final: 0.7985 (p)
REVERT: A  399 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6684 (mt-10)
REVERT: A  413 GLU cc_start: 0.7274 (tt0) cc_final: 0.7045 (tt0)
REVERT: A  416 SER cc_start: 0.8890 (m) cc_final: 0.8403 (p)
REVERT: A  427 ILE cc_start: 0.8130 (mt) cc_final: 0.7711 (tp)
REVERT: A  433 GLU cc_start: 0.7655 (mp0) cc_final: 0.7065 (mp0)
REVERT: A  437 TRP cc_start: 0.8378 (m100) cc_final: 0.7609 (m-10)
REVERT: H   13 LYS cc_start: 0.7592 (mtmm) cc_final: 0.7350 (mtmm)
REVERT: H   25 TYR cc_start: 0.7900 (m-10) cc_final: 0.7694 (m-10)
REVERT: H   31 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6873 (p90)
REVERT: H   99 TYR cc_start: 0.7904 (m-80) cc_final: 0.7553 (m-80)
REVERT: H  100 HIS cc_start: 0.7391 (t-90) cc_final: 0.6956 (t-90)
REVERT: H  100 LEU cc_start: 0.7952 (mt) cc_final: 0.7184 (mt)
REVERT: H  100 TYR cc_start: 0.8069 (m-80) cc_final: 0.7577 (m-80)
REVERT: L    4 MET cc_start: 0.5453 (mpp) cc_final: 0.5229 (mpp)
REVERT: L    7 SER cc_start: 0.8490 (m) cc_final: 0.8123 (p)
REVERT: L   10 SER cc_start: 0.7928 (t) cc_final: 0.7703 (m)
REVERT: L   58 VAL cc_start: 0.8800 (t) cc_final: 0.8526 (p)
REVERT: L  103 LYS cc_start: 0.7797 (tttt) cc_final: 0.7460 (tttt)
REVERT: M   32 TYR cc_start: 0.7618 (m-10) cc_final: 0.7385 (m-10)
REVERT: M   59 TYR cc_start: 0.8192 (m-10) cc_final: 0.7835 (m-80)
REVERT: M   96 SER cc_start: 0.8308 (m) cc_final: 0.7975 (p)
REVERT: N   49 TYR cc_start: 0.8564 (p90) cc_final: 0.8321 (p90)
REVERT: N   56 SER cc_start: 0.8666 (t) cc_final: 0.8321 (p)
REVERT: N   82 ASP cc_start: 0.8155 (m-30) cc_final: 0.7713 (m-30)
  outliers start: 19
  outliers final: 10
  residues processed: 268
  average time/residue: 0.0828
  time to fit residues: 29.0032
Evaluate side-chains
  249 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 236
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  261 LYS
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0970
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
A  93 ASN
A 226 GLN
A 273 GLN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  53 HIS
L  55 GLN
M  73 ASN
N  90 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.106582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.094023 restraints weight = 11772.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.097230 restraints weight = 4925.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.099197 restraints weight = 2508.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.100433 restraints weight = 1475.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.101104 restraints weight = 973.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6783  Z= 0.118
  Angle     :  0.609   7.289   9226  Z= 0.313
  Chirality :  0.045   0.157    997
  Planarity :  0.005   0.042   1179
  Dihedral  :  5.637  53.347    958
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.25 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.27), residues: 841
  helix: -2.95 (1.40), residues: 6
  sheet: -1.22 (0.29), residues: 321
  loop : -2.73 (0.24), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M  94 
 TYR   0.025   0.002   TYR M 100A
 PHE   0.013   0.001   PHE H  78 
 TRP   0.028   0.001   TRP H   7 
 HIS   0.002   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6769)
  covalent geometry    : angle       0.60600 ( 9197)
  SS BOND              : bond        0.00324 (   13)
  SS BOND              : angle       0.98778 (   26)
  hydrogen bonds       : bond        0.03705 (  151)
  hydrogen bonds       : angle       5.78304 (  423)
  link_NAG-ASN         : bond        0.00110 (    1)
  link_NAG-ASN         : angle       2.85730 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 254
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8251 (mttt) cc_final: 0.7851 (mmtt)
REVERT: A  104 ASN cc_start: 0.8317 (m-40) cc_final: 0.8012 (m110)
REVERT: A  119 GLU cc_start: 0.7453 (mp0) cc_final: 0.7210 (mp0)
REVERT: A  128 LYS cc_start: 0.7977 (pttm) cc_final: 0.7425 (pttm)
REVERT: A  142 ASN cc_start: 0.7984 (t0) cc_final: 0.7668 (t0)
REVERT: A  162 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7265 (mt-10)
REVERT: A  245 SER cc_start: 0.8527 (t) cc_final: 0.8030 (p)
REVERT: A  249 LYS cc_start: 0.8361 (mttt) cc_final: 0.7540 (mtpp)
REVERT: A  251 ASP cc_start: 0.7495 (m-30) cc_final: 0.7140 (m-30)
REVERT: A  258 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6938 (mt-10)
REVERT: A  292 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7350 (ptt180)
REVERT: A  302 ILE cc_start: 0.8642 (mt) cc_final: 0.8116 (mm)
REVERT: A  307 VAL cc_start: 0.8641 (m) cc_final: 0.8349 (t)
REVERT: A  327 ARG cc_start: 0.8288 (ptt-90) cc_final: 0.8030 (ptt-90)
REVERT: A  343 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6793 (mp0)
REVERT: A  356 ASP cc_start: 0.8196 (t0) cc_final: 0.7924 (t0)
REVERT: A  370 LEU cc_start: 0.8697 (mt) cc_final: 0.8382 (mm)
REVERT: A  375 GLU cc_start: 0.7698 (pt0) cc_final: 0.7113 (pt0)
REVERT: A  378 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7749 (ttpp)
REVERT: A  385 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8000 (mtpp)
REVERT: A  388 SER cc_start: 0.8469 (t) cc_final: 0.7972 (p)
REVERT: A  389 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8448 (mttp)
REVERT: A  399 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6735 (mt-10)
REVERT: A  403 ARG cc_start: 0.7878 (mtp180) cc_final: 0.6273 (mtm180)
REVERT: A  413 GLU cc_start: 0.7328 (tt0) cc_final: 0.7065 (tt0)
REVERT: A  416 SER cc_start: 0.8901 (m) cc_final: 0.8407 (p)
REVERT: A  427 ILE cc_start: 0.8114 (mt) cc_final: 0.7501 (tp)
REVERT: A  432 GLU cc_start: 0.7237 (mp0) cc_final: 0.6723 (mp0)
REVERT: A  433 GLU cc_start: 0.7715 (mp0) cc_final: 0.6792 (mp0)
REVERT: A  437 TRP cc_start: 0.8317 (m100) cc_final: 0.7500 (m-10)
REVERT: H   13 LYS cc_start: 0.7639 (mtmm) cc_final: 0.7409 (mtmm)
REVERT: H   67 VAL cc_start: 0.8768 (t) cc_final: 0.8523 (m)
REVERT: H   99 TYR cc_start: 0.7966 (m-80) cc_final: 0.7660 (m-80)
REVERT: H  100 HIS cc_start: 0.7301 (t-90) cc_final: 0.6866 (t-90)
REVERT: H  100 LEU cc_start: 0.8066 (mt) cc_final: 0.7324 (mt)
REVERT: L    7 SER cc_start: 0.8576 (m) cc_final: 0.8195 (p)
REVERT: L   33 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5519 (tm)
REVERT: L   58 VAL cc_start: 0.8808 (t) cc_final: 0.8518 (p)
REVERT: L  103 LYS cc_start: 0.7794 (tttt) cc_final: 0.7380 (tttt)
REVERT: L  107 LYS cc_start: 0.7602 (pttp) cc_final: 0.7196 (tppt)
REVERT: M   32 TYR cc_start: 0.7770 (m-80) cc_final: 0.7365 (m-10)
REVERT: M   59 TYR cc_start: 0.8272 (m-10) cc_final: 0.8010 (m-80)
REVERT: M   83 LYS cc_start: 0.8402 (mttt) cc_final: 0.8167 (ttmm)
REVERT: M   96 SER cc_start: 0.8299 (m) cc_final: 0.7966 (p)
REVERT: N   49 TYR cc_start: 0.8528 (p90) cc_final: 0.8297 (p90)
REVERT: N   56 SER cc_start: 0.8674 (t) cc_final: 0.8337 (p)
REVERT: N   67 TYR cc_start: 0.8318 (t80) cc_final: 0.7974 (t80)
REVERT: N   82 ASP cc_start: 0.8157 (m-30) cc_final: 0.7925 (m-30)
  outliers start: 25
  outliers final: 13
  residues processed: 264
  average time/residue: 0.0721
  time to fit residues: 24.9358
Evaluate side-chains
  261 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 245
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   53 HIS
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain M residue   18 LEU
Chi-restraints excluded: chain M residue   57 THR
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  53 ASN
N  90 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.104024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.091619 restraints weight = 11971.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.094817 restraints weight = 4981.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.096748 restraints weight = 2515.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.097918 restraints weight = 1460.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.098635 restraints weight = 967.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6783  Z= 0.214
  Angle     :  0.659   8.674   9226  Z= 0.345
  Chirality :  0.047   0.164    997
  Planarity :  0.005   0.053   1179
  Dihedral  :  5.650  45.567    954
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 16.39 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.05 (0.27), residues: 841
  helix: -2.70 (2.11), residues: 6
  sheet: -1.22 (0.27), residues: 359
  loop : -2.76 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 292 
 TYR   0.022   0.002   TYR M  32 
 PHE   0.022   0.002   PHE H  78 
 TRP   0.035   0.002   TRP H   7 
 HIS   0.011   0.002   HIS H  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6769)
  covalent geometry    : angle       0.65518 ( 9197)
  SS BOND              : bond        0.00436 (   13)
  SS BOND              : angle       1.06410 (   26)
  hydrogen bonds       : bond        0.04283 (  151)
  hydrogen bonds       : angle       5.96886 (  423)
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       3.24852 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 255
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8312 (mttt) cc_final: 0.7922 (mmtt)
REVERT: A  102 LYS cc_start: 0.8409 (tttp) cc_final: 0.8148 (tttt)
REVERT: A  104 ASN cc_start: 0.8308 (m-40) cc_final: 0.7945 (m-40)
REVERT: A  128 LYS cc_start: 0.8000 (pttm) cc_final: 0.7647 (pttm)
REVERT: A  160 MET cc_start: 0.7569 (ttt) cc_final: 0.7282 (ttm)
REVERT: A  245 SER cc_start: 0.8573 (t) cc_final: 0.8070 (p)
REVERT: A  249 LYS cc_start: 0.8418 (mttt) cc_final: 0.7925 (mttt)
REVERT: A  251 ASP cc_start: 0.7603 (m-30) cc_final: 0.7243 (m-30)
REVERT: A  258 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6900 (mt-10)
REVERT: A  276 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6703 (mm-30)
REVERT: A  292 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7297 (ptt180)
REVERT: A  302 ILE cc_start: 0.8749 (mt) cc_final: 0.8264 (mm)
REVERT: A  307 VAL cc_start: 0.8684 (m) cc_final: 0.8378 (t)
REVERT: A  309 ASN cc_start: 0.7441 (t0) cc_final: 0.7064 (t0)
REVERT: A  327 ARG cc_start: 0.8286 (ptt-90) cc_final: 0.8070 (ptt-90)
REVERT: A  343 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6804 (mp0)
REVERT: A  356 ASP cc_start: 0.8269 (t0) cc_final: 0.8059 (t0)
REVERT: A  370 LEU cc_start: 0.8769 (mt) cc_final: 0.8543 (mm)
REVERT: A  375 GLU cc_start: 0.7644 (pt0) cc_final: 0.7080 (pt0)
REVERT: A  385 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8059 (mtpp)
REVERT: A  388 SER cc_start: 0.8559 (t) cc_final: 0.8027 (p)
REVERT: A  389 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8585 (mtpp)
REVERT: A  413 GLU cc_start: 0.7307 (tt0) cc_final: 0.7022 (tt0)
REVERT: A  416 SER cc_start: 0.8927 (m) cc_final: 0.8433 (p)
REVERT: A  427 ILE cc_start: 0.8186 (mt) cc_final: 0.7939 (tt)
REVERT: A  433 GLU cc_start: 0.7706 (mp0) cc_final: 0.7028 (mp0)
REVERT: A  437 TRP cc_start: 0.8369 (m100) cc_final: 0.7447 (m-10)
REVERT: H   13 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7334 (mtmm)
REVERT: H   16 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7299 (mt-10)
REVERT: H   99 TYR cc_start: 0.7912 (m-80) cc_final: 0.7511 (m-80)
REVERT: H  100 LEU cc_start: 0.8211 (mt) cc_final: 0.7873 (mp)
REVERT: L    7 SER cc_start: 0.8726 (m) cc_final: 0.8277 (p)
REVERT: L   22 THR cc_start: 0.7763 (p) cc_final: 0.7394 (p)
REVERT: L   58 VAL cc_start: 0.8815 (t) cc_final: 0.8525 (p)
REVERT: L  103 LYS cc_start: 0.7979 (tttt) cc_final: 0.7385 (tttt)
REVERT: M   32 TYR cc_start: 0.7782 (m-80) cc_final: 0.7533 (m-10)
REVERT: M   59 TYR cc_start: 0.8283 (m-10) cc_final: 0.7975 (m-80)
REVERT: M   83 LYS cc_start: 0.8422 (mttt) cc_final: 0.8064 (ttmm)
REVERT: M   96 SER cc_start: 0.8343 (m) cc_final: 0.7935 (p)
REVERT: M  100 TYR cc_start: 0.7762 (t80) cc_final: 0.7462 (t80)
REVERT: N   56 SER cc_start: 0.8644 (t) cc_final: 0.8325 (p)
REVERT: N   67 TYR cc_start: 0.8369 (t80) cc_final: 0.8048 (t80)
  outliers start: 35
  outliers final: 28
  residues processed: 270
  average time/residue: 0.0844
  time to fit residues: 29.6282
Evaluate side-chains
  274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 244
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   66 ARG
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   18 LEU
Chi-restraints excluded: chain M residue   57 THR
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain N residue   17 ASP
Chi-restraints excluded: chain N residue   75 ILE
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 60 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 53 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.3320

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  53 HIS
N  90 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.104653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.092267 restraints weight = 12001.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.095443 restraints weight = 4997.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.097393 restraints weight = 2527.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.098574 restraints weight = 1471.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.099240 restraints weight = 978.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6783  Z= 0.185
  Angle     :  0.656   8.634   9226  Z= 0.339
  Chirality :  0.047   0.166    997
  Planarity :  0.005   0.048   1179
  Dihedral  :  5.506  43.453    954
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 17.77 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.27), residues: 841
  helix: -2.43 (2.42), residues: 6
  sheet: -1.10 (0.28), residues: 348
  loop : -2.64 (0.25), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  24 
 TYR   0.029   0.002   TYR N  49 
 PHE   0.021   0.002   PHE H  78 
 TRP   0.030   0.002   TRP H   7 
 HIS   0.005   0.001   HIS H  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6769)
  covalent geometry    : angle       0.65161 ( 9197)
  SS BOND              : bond        0.00438 (   13)
  SS BOND              : angle       1.24218 (   26)
  hydrogen bonds       : bond        0.03958 (  151)
  hydrogen bonds       : angle       5.88630 (  423)
  link_NAG-ASN         : bond        0.00154 (    1)
  link_NAG-ASN         : angle       3.19744 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 245
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8300 (mttt) cc_final: 0.7923 (mmtt)
REVERT: A  104 ASN cc_start: 0.8264 (m-40) cc_final: 0.8029 (m-40)
REVERT: A  160 MET cc_start: 0.7566 (ttt) cc_final: 0.7272 (ttm)
REVERT: A  245 SER cc_start: 0.8545 (t) cc_final: 0.8073 (p)
REVERT: A  249 LYS cc_start: 0.8421 (mttt) cc_final: 0.8208 (mttt)
REVERT: A  251 ASP cc_start: 0.7631 (m-30) cc_final: 0.7267 (m-30)
REVERT: A  258 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6915 (mt-10)
REVERT: A  292 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7567 (ptt180)
REVERT: A  302 ILE cc_start: 0.8760 (mt) cc_final: 0.8287 (mm)
REVERT: A  306 ASN cc_start: 0.7967 (t0) cc_final: 0.7650 (t0)
REVERT: A  307 VAL cc_start: 0.8653 (m) cc_final: 0.8222 (t)
REVERT: A  309 ASN cc_start: 0.7379 (t0) cc_final: 0.7036 (t0)
REVERT: A  343 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6765 (mp0)
REVERT: A  375 GLU cc_start: 0.7625 (pt0) cc_final: 0.7055 (pt0)
REVERT: A  378 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7759 (ttpp)
REVERT: A  385 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8081 (mtpp)
REVERT: A  388 SER cc_start: 0.8556 (t) cc_final: 0.8026 (p)
REVERT: A  389 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8545 (mtpp)
REVERT: A  403 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7594 (mtm180)
REVERT: A  413 GLU cc_start: 0.7280 (tt0) cc_final: 0.6995 (tt0)
REVERT: A  416 SER cc_start: 0.8942 (m) cc_final: 0.8440 (p)
REVERT: A  427 ILE cc_start: 0.8255 (mt) cc_final: 0.7307 (tt)
REVERT: A  433 GLU cc_start: 0.7730 (mp0) cc_final: 0.7294 (mp0)
REVERT: A  437 TRP cc_start: 0.8333 (m100) cc_final: 0.7424 (m-10)
REVERT: H    7 TRP cc_start: 0.7532 (p-90) cc_final: 0.7304 (p-90)
REVERT: H   13 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7379 (mtmm)
REVERT: H   16 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7296 (mt-10)
REVERT: H   99 TYR cc_start: 0.7892 (m-80) cc_final: 0.7477 (m-80)
REVERT: H  100 LEU cc_start: 0.8130 (mt) cc_final: 0.7875 (mp)
REVERT: L    7 SER cc_start: 0.8702 (m) cc_final: 0.8272 (p)
REVERT: L   58 VAL cc_start: 0.8840 (t) cc_final: 0.8531 (p)
REVERT: L  103 LYS cc_start: 0.7981 (tttt) cc_final: 0.7423 (tttt)
REVERT: M   32 TYR cc_start: 0.7783 (m-80) cc_final: 0.7548 (m-10)
REVERT: M   59 TYR cc_start: 0.8297 (m-10) cc_final: 0.8048 (m-80)
REVERT: M   83 LYS cc_start: 0.8397 (mttt) cc_final: 0.8073 (ttmm)
REVERT: M   96 SER cc_start: 0.8372 (m) cc_final: 0.7939 (p)
REVERT: M  100 TYR cc_start: 0.7806 (t80) cc_final: 0.7510 (t80)
REVERT: N   24 ARG cc_start: 0.7111 (ttm170) cc_final: 0.6671 (ttm110)
REVERT: N   27 GLN cc_start: 0.7314 (pt0) cc_final: 0.7108 (pt0)
REVERT: N   56 SER cc_start: 0.8657 (t) cc_final: 0.8339 (p)
REVERT: N   67 TYR cc_start: 0.8402 (t80) cc_final: 0.8003 (t80)
REVERT: N   89 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7185 (tt0)
  outliers start: 36
  outliers final: 28
  residues processed: 259
  average time/residue: 0.0815
  time to fit residues: 27.4969
Evaluate side-chains
  271 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 241
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   60 ILE
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   18 LEU
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain N residue   17 ASP
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   53 LEU
Chi-restraints excluded: chain N residue   54 LEU
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0970
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** 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 = 0.3327 r_free = 0.3327 target = 0.105641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.093210 restraints weight = 11983.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.096424 restraints weight = 5004.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.098372 restraints weight = 2531.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.099567 restraints weight = 1472.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.100319 restraints weight = 978.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6783  Z= 0.142
  Angle     :  0.626   8.467   9226  Z= 0.321
  Chirality :  0.047   0.170    997
  Planarity :  0.005   0.044   1179
  Dihedral  :  5.265  43.861    954
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 19.15 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.27), residues: 841
  helix: -2.57 (2.21), residues: 6
  sheet: -1.10 (0.29), residues: 344
  loop : -2.48 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  24 
 TYR   0.017   0.001   TYR N  94 
 PHE   0.018   0.001   PHE H  78 
 TRP   0.025   0.002   TRP H   7 
 HIS   0.002   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6769)
  covalent geometry    : angle       0.62192 ( 9197)
  SS BOND              : bond        0.00371 (   13)
  SS BOND              : angle       1.10965 (   26)
  hydrogen bonds       : bond        0.03555 (  151)
  hydrogen bonds       : angle       5.70746 (  423)
  link_NAG-ASN         : bond        0.00196 (    1)
  link_NAG-ASN         : angle       2.69553 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 243
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8283 (mttt) cc_final: 0.7884 (mmtt)
REVERT: A  104 ASN cc_start: 0.8217 (m-40) cc_final: 0.7942 (m-40)
REVERT: A  245 SER cc_start: 0.8509 (t) cc_final: 0.8182 (p)
REVERT: A  249 LYS cc_start: 0.8418 (mttt) cc_final: 0.7979 (mttt)
REVERT: A  251 ASP cc_start: 0.7621 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  292 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7133 (ptt180)
REVERT: A  302 ILE cc_start: 0.8756 (mt) cc_final: 0.8263 (mm)
REVERT: A  307 VAL cc_start: 0.8601 (m) cc_final: 0.8281 (t)
REVERT: A  309 ASN cc_start: 0.7410 (t0) cc_final: 0.6986 (t0)
REVERT: A  343 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6731 (mp0)
REVERT: A  370 LEU cc_start: 0.8740 (mt) cc_final: 0.8510 (mm)
REVERT: A  375 GLU cc_start: 0.7621 (pt0) cc_final: 0.7051 (pt0)
REVERT: A  378 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7735 (ttpp)
REVERT: A  385 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8015 (mtpp)
REVERT: A  388 SER cc_start: 0.8571 (t) cc_final: 0.8047 (p)
REVERT: A  389 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8538 (mtpp)
REVERT: A  413 GLU cc_start: 0.7238 (tt0) cc_final: 0.7008 (tt0)
REVERT: A  416 SER cc_start: 0.8939 (m) cc_final: 0.8474 (p)
REVERT: A  427 ILE cc_start: 0.8177 (mt) cc_final: 0.7863 (tt)
REVERT: A  433 GLU cc_start: 0.7724 (mp0) cc_final: 0.7133 (mp0)
REVERT: A  437 TRP cc_start: 0.8298 (m100) cc_final: 0.7372 (m-10)
REVERT: H   13 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7330 (mtmm)
REVERT: H   16 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7161 (mt-10)
REVERT: H   99 TYR cc_start: 0.7902 (m-80) cc_final: 0.7535 (m-80)
REVERT: H  100 LEU cc_start: 0.7979 (mt) cc_final: 0.7729 (mp)
REVERT: L    7 SER cc_start: 0.8647 (m) cc_final: 0.8264 (p)
REVERT: L   42 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8218 (mmmt)
REVERT: L   58 VAL cc_start: 0.8821 (t) cc_final: 0.8514 (p)
REVERT: L  103 LYS cc_start: 0.7966 (tttt) cc_final: 0.7400 (tttt)
REVERT: M   32 TYR cc_start: 0.7747 (m-80) cc_final: 0.7498 (m-10)
REVERT: M   59 TYR cc_start: 0.8317 (m-10) cc_final: 0.8082 (m-80)
REVERT: M   83 LYS cc_start: 0.8361 (mttt) cc_final: 0.8078 (ttmm)
REVERT: M   96 SER cc_start: 0.8365 (m) cc_final: 0.7972 (p)
REVERT: M  100 TYR cc_start: 0.7824 (t80) cc_final: 0.7492 (t80)
REVERT: N   24 ARG cc_start: 0.7053 (ttm170) cc_final: 0.6757 (ttm170)
REVERT: N   27 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.7042 (pt0)
REVERT: N   56 SER cc_start: 0.8640 (t) cc_final: 0.8331 (p)
REVERT: N   67 TYR cc_start: 0.8439 (t80) cc_final: 0.7896 (t80)
REVERT: N   89 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7219 (tt0)
  outliers start: 33
  outliers final: 26
  residues processed: 259
  average time/residue: 0.0746
  time to fit residues: 25.4094
Evaluate side-chains
  269 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 240
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   53 HIS
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   18 LEU
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain N residue   27 GLN
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   53 LEU
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0870
   chunk 44 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 60 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  90 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.103270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.091238 restraints weight = 11858.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.094308 restraints weight = 4950.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.096174 restraints weight = 2505.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.097308 restraints weight = 1464.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.097997 restraints weight = 977.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.111   6783  Z= 0.272
  Angle     :  0.751  10.363   9226  Z= 0.388
  Chirality :  0.050   0.283    997
  Planarity :  0.006   0.054   1179
  Dihedral  :  5.711  38.917    954
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 19.56 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.27), residues: 841
  helix: -2.42 (2.57), residues: 6
  sheet: -1.19 (0.29), residues: 331
  loop : -2.62 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  24 
 TYR   0.034   0.002   TYR N  49 
 PHE   0.028   0.002   PHE H  78 
 TRP   0.046   0.002   TRP H   7 
 HIS   0.006   0.002   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 6769)
  covalent geometry    : angle       0.73746 ( 9197)
  SS BOND              : bond        0.00754 (   13)
  SS BOND              : angle       2.52415 (   26)
  hydrogen bonds       : bond        0.04609 (  151)
  hydrogen bonds       : angle       6.06354 (  423)
  link_NAG-ASN         : bond        0.00220 (    1)
  link_NAG-ASN         : angle       3.56673 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 251
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8302 (mttt) cc_final: 0.7949 (mmtt)
REVERT: A  251 ASP cc_start: 0.7577 (m-30) cc_final: 0.7267 (m-30)
REVERT: A  258 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6770 (mt-10)
REVERT: A  292 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7146 (ptt180)
REVERT: A  302 ILE cc_start: 0.8763 (mt) cc_final: 0.8306 (mm)
REVERT: A  307 VAL cc_start: 0.8642 (m) cc_final: 0.8371 (t)
REVERT: A  309 ASN cc_start: 0.7327 (t0) cc_final: 0.6926 (t0)
REVERT: A  327 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.8130 (ptt-90)
REVERT: A  343 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6778 (mp0)
REVERT: A  375 GLU cc_start: 0.7614 (pt0) cc_final: 0.7084 (pt0)
REVERT: A  378 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7733 (ttpp)
REVERT: A  385 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8108 (mtpp)
REVERT: A  388 SER cc_start: 0.8533 (t) cc_final: 0.8008 (p)
REVERT: A  399 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6690 (mt-10)
REVERT: A  413 GLU cc_start: 0.7273 (tt0) cc_final: 0.7029 (tt0)
REVERT: A  416 SER cc_start: 0.8949 (m) cc_final: 0.8467 (p)
REVERT: A  427 ILE cc_start: 0.8329 (mt) cc_final: 0.7873 (tt)
REVERT: A  433 GLU cc_start: 0.7705 (mp0) cc_final: 0.7064 (mp0)
REVERT: A  437 TRP cc_start: 0.8319 (m100) cc_final: 0.7332 (m-10)
REVERT: H   13 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7442 (mtmm)
REVERT: H   16 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7311 (mt-10)
REVERT: H   22 CYS cc_start: 0.5939 (t) cc_final: 0.5739 (t)
REVERT: H   50 GLU cc_start: 0.7226 (pt0) cc_final: 0.6987 (pt0)
REVERT: H   99 TYR cc_start: 0.7921 (m-80) cc_final: 0.7447 (m-80)
REVERT: H  100 LEU cc_start: 0.8090 (mt) cc_final: 0.7851 (mp)
REVERT: L    7 SER cc_start: 0.8745 (m) cc_final: 0.8333 (p)
REVERT: L   42 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8099 (mmmt)
REVERT: L   58 VAL cc_start: 0.8888 (t) cc_final: 0.8579 (p)
REVERT: L  103 LYS cc_start: 0.8083 (tttt) cc_final: 0.7509 (tttt)
REVERT: M   32 TYR cc_start: 0.7832 (m-80) cc_final: 0.7632 (m-10)
REVERT: M   83 LYS cc_start: 0.8396 (mttt) cc_final: 0.8111 (ttmm)
REVERT: M  100 TYR cc_start: 0.7787 (t80) cc_final: 0.7570 (t80)
REVERT: N    9 SER cc_start: 0.8722 (m) cc_final: 0.8385 (t)
REVERT: N   27 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6965 (pt0)
REVERT: N   56 SER cc_start: 0.8642 (t) cc_final: 0.8349 (p)
REVERT: N   67 TYR cc_start: 0.8437 (t80) cc_final: 0.7950 (t80)
REVERT: N   89 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7217 (tt0)
  outliers start: 41
  outliers final: 33
  residues processed: 267
  average time/residue: 0.0721
  time to fit residues: 25.3749
Evaluate side-chains
  280 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 244
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   53 HIS
Chi-restraints excluded: chain H residue   66 ARG
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   18 LEU
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain M residue  102 LEU
Chi-restraints excluded: chain N residue   17 ASP
Chi-restraints excluded: chain N residue   27 GLN
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   53 LEU
Chi-restraints excluded: chain N residue   54 LEU
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 104 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  90 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.105602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.093337 restraints weight = 12044.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.096488 restraints weight = 5063.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.098407 restraints weight = 2578.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.099591 restraints weight = 1506.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.100313 restraints weight = 1001.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.118   6783  Z= 0.148
  Angle     :  0.699  12.784   9226  Z= 0.353
  Chirality :  0.048   0.228    997
  Planarity :  0.005   0.043   1179
  Dihedral  :  5.341  40.874    954
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 22.18 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.28), residues: 841
  helix: -2.20 (2.57), residues: 6
  sheet: -1.00 (0.29), residues: 336
  loop : -2.42 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 327 
 TYR   0.014   0.001   TYR N  49 
 PHE   0.018   0.002   PHE H  78 
 TRP   0.040   0.002   TRP H   7 
 HIS   0.005   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6769)
  covalent geometry    : angle       0.68289 ( 9197)
  SS BOND              : bond        0.00820 (   13)
  SS BOND              : angle       2.72774 (   26)
  hydrogen bonds       : bond        0.03478 (  151)
  hydrogen bonds       : angle       5.78770 (  423)
  link_NAG-ASN         : bond        0.00189 (    1)
  link_NAG-ASN         : angle       2.75863 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 248
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8286 (mttt) cc_final: 0.7852 (mmtt)
REVERT: A  245 SER cc_start: 0.8501 (t) cc_final: 0.8095 (p)
REVERT: A  251 ASP cc_start: 0.7489 (m-30) cc_final: 0.7210 (m-30)
REVERT: A  258 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6742 (mt-10)
REVERT: A  292 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7283 (ptt180)
REVERT: A  302 ILE cc_start: 0.8780 (mt) cc_final: 0.8296 (mm)
REVERT: A  307 VAL cc_start: 0.8554 (m) cc_final: 0.8274 (t)
REVERT: A  309 ASN cc_start: 0.7371 (t0) cc_final: 0.6936 (t0)
REVERT: A  343 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6743 (mp0)
REVERT: A  375 GLU cc_start: 0.7591 (pt0) cc_final: 0.7130 (pt0)
REVERT: A  378 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7715 (ttpp)
REVERT: A  385 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7990 (mtpp)
REVERT: A  388 SER cc_start: 0.8532 (t) cc_final: 0.8010 (p)
REVERT: A  403 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7487 (mtm180)
REVERT: A  413 GLU cc_start: 0.7234 (tt0) cc_final: 0.7002 (tt0)
REVERT: A  416 SER cc_start: 0.8942 (m) cc_final: 0.8475 (p)
REVERT: A  427 ILE cc_start: 0.8235 (mt) cc_final: 0.7283 (tt)
REVERT: A  433 GLU cc_start: 0.7714 (mp0) cc_final: 0.7264 (mp0)
REVERT: A  437 TRP cc_start: 0.8268 (m100) cc_final: 0.7320 (m-10)
REVERT: H   13 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7359 (mtmm)
REVERT: H   16 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7161 (mt-10)
REVERT: H   99 TYR cc_start: 0.7918 (m-80) cc_final: 0.7546 (m-80)
REVERT: L    7 SER cc_start: 0.8670 (m) cc_final: 0.8280 (p)
REVERT: L   42 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8054 (mmmt)
REVERT: L   58 VAL cc_start: 0.8852 (t) cc_final: 0.8547 (p)
REVERT: L  103 LYS cc_start: 0.8004 (tttt) cc_final: 0.7400 (tttt)
REVERT: M   32 TYR cc_start: 0.7743 (m-80) cc_final: 0.7501 (m-10)
REVERT: M   59 TYR cc_start: 0.8482 (m-80) cc_final: 0.8141 (m-80)
REVERT: M   83 LYS cc_start: 0.8311 (mttt) cc_final: 0.8071 (ttmm)
REVERT: M   96 SER cc_start: 0.8338 (m) cc_final: 0.8066 (p)
REVERT: M  100 TYR cc_start: 0.7769 (t80) cc_final: 0.7478 (t80)
REVERT: N   24 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6907 (ttm170)
REVERT: N   56 SER cc_start: 0.8644 (t) cc_final: 0.8345 (p)
REVERT: N   89 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7208 (tt0)
  outliers start: 34
  outliers final: 28
  residues processed: 263
  average time/residue: 0.0762
  time to fit residues: 26.1602
Evaluate side-chains
  272 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 242
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   53 HIS
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain M residue  102 LEU
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   53 LEU
Chi-restraints excluded: chain N residue   54 LEU
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0270
   chunk 53 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 184 HIS
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.106164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.094071 restraints weight = 12101.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.097168 restraints weight = 5117.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.099039 restraints weight = 2607.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.100208 restraints weight = 1533.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.100936 restraints weight = 1017.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   6783  Z= 0.133
  Angle     :  0.696  13.142   9226  Z= 0.350
  Chirality :  0.048   0.212    997
  Planarity :  0.005   0.038   1179
  Dihedral  :  5.188  40.289    954
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 23.00 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.55 (0.28), residues: 841
  helix: -2.67 (2.08), residues: 6
  sheet: -0.92 (0.29), residues: 339
  loop : -2.34 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  24 
 TYR   0.029   0.001   TYR N  49 
 PHE   0.019   0.001   PHE A 410 
 TRP   0.042   0.002   TRP H   7 
 HIS   0.004   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6769)
  covalent geometry    : angle       0.67808 ( 9197)
  SS BOND              : bond        0.00767 (   13)
  SS BOND              : angle       2.89409 (   26)
  hydrogen bonds       : bond        0.03315 (  151)
  hydrogen bonds       : angle       5.63544 (  423)
  link_NAG-ASN         : bond        0.00152 (    1)
  link_NAG-ASN         : angle       2.48281 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 243
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8280 (mttt) cc_final: 0.7874 (mmtt)
REVERT: A  245 SER cc_start: 0.8446 (t) cc_final: 0.8155 (p)
REVERT: A  251 ASP cc_start: 0.7487 (m-30) cc_final: 0.7219 (m-30)
REVERT: A  258 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6801 (mt-10)
REVERT: A  292 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7275 (ptt180)
REVERT: A  302 ILE cc_start: 0.8772 (mt) cc_final: 0.8278 (mm)
REVERT: A  307 VAL cc_start: 0.8511 (m) cc_final: 0.8221 (t)
REVERT: A  309 ASN cc_start: 0.7372 (t0) cc_final: 0.6949 (t0)
REVERT: A  343 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6753 (mp0)
REVERT: A  375 GLU cc_start: 0.7582 (pt0) cc_final: 0.7097 (pt0)
REVERT: A  378 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7716 (ttpp)
REVERT: A  385 LYS cc_start: 0.8343 (mmmt) cc_final: 0.7993 (mtpp)
REVERT: A  388 SER cc_start: 0.8568 (t) cc_final: 0.8012 (p)
REVERT: A  389 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8463 (mttm)
REVERT: A  399 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6678 (mt-10)
REVERT: A  403 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7326 (mtm180)
REVERT: A  413 GLU cc_start: 0.7261 (tt0) cc_final: 0.7046 (tt0)
REVERT: A  416 SER cc_start: 0.8939 (m) cc_final: 0.8468 (p)
REVERT: A  427 ILE cc_start: 0.8179 (mt) cc_final: 0.7396 (tt)
REVERT: A  433 GLU cc_start: 0.7695 (mp0) cc_final: 0.7236 (mp0)
REVERT: A  437 TRP cc_start: 0.8266 (m100) cc_final: 0.7403 (m-10)
REVERT: H   13 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7279 (mtmm)
REVERT: H   16 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7053 (mt-10)
REVERT: H   33 PHE cc_start: 0.7655 (m-80) cc_final: 0.7428 (m-10)
REVERT: H   99 TYR cc_start: 0.7932 (m-80) cc_final: 0.7617 (m-80)
REVERT: L    7 SER cc_start: 0.8643 (m) cc_final: 0.8240 (p)
REVERT: L   24 ARG cc_start: 0.7157 (mmm160) cc_final: 0.6921 (mmm160)
REVERT: L   42 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8015 (mmmt)
REVERT: L   58 VAL cc_start: 0.8815 (t) cc_final: 0.8527 (p)
REVERT: L  103 LYS cc_start: 0.8018 (tttt) cc_final: 0.7428 (tttt)
REVERT: M   32 TYR cc_start: 0.7735 (m-80) cc_final: 0.7478 (m-10)
REVERT: M   59 TYR cc_start: 0.8508 (m-80) cc_final: 0.8131 (m-80)
REVERT: M   83 LYS cc_start: 0.8386 (mttt) cc_final: 0.8093 (ttmm)
REVERT: M   96 SER cc_start: 0.8343 (m) cc_final: 0.8088 (p)
REVERT: M  100 TYR cc_start: 0.7729 (t80) cc_final: 0.7477 (t80)
REVERT: N   56 SER cc_start: 0.8643 (t) cc_final: 0.8357 (p)
REVERT: N   89 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7152 (tt0)
  outliers start: 34
  outliers final: 27
  residues processed: 257
  average time/residue: 0.0753
  time to fit residues: 25.3718
Evaluate side-chains
  270 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 241
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   53 HIS
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain M residue  102 LEU
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0970
   chunk 21 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 104 ASN
A 342 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.106472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.094326 restraints weight = 12050.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.097432 restraints weight = 5100.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.099320 restraints weight = 2608.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.100498 restraints weight = 1531.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.101193 restraints weight = 1012.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.113   6783  Z= 0.133
  Angle     :  0.683  12.699   9226  Z= 0.344
  Chirality :  0.047   0.220    997
  Planarity :  0.004   0.036   1179
  Dihedral  :  5.081  39.892    954
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 23.83 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.28), residues: 841
  helix: -2.42 (2.28), residues: 6
  sheet: -0.80 (0.29), residues: 334
  loop : -2.30 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  24 
 TYR   0.014   0.001   TYR N  49 
 PHE   0.020   0.001   PHE A 410 
 TRP   0.040   0.002   TRP H   7 
 HIS   0.003   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6769)
  covalent geometry    : angle       0.66543 ( 9197)
  SS BOND              : bond        0.00772 (   13)
  SS BOND              : angle       2.82720 (   26)
  hydrogen bonds       : bond        0.03253 (  151)
  hydrogen bonds       : angle       5.56161 (  423)
  link_NAG-ASN         : bond        0.00139 (    1)
  link_NAG-ASN         : angle       2.43353 (    3)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 238
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8289 (mttt) cc_final: 0.7856 (mmtt)
REVERT: A  245 SER cc_start: 0.8463 (t) cc_final: 0.8158 (p)
REVERT: A  251 ASP cc_start: 0.7495 (m-30) cc_final: 0.7230 (m-30)
REVERT: A  258 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6819 (mt-10)
REVERT: A  292 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7133 (ptt180)
REVERT: A  302 ILE cc_start: 0.8774 (mt) cc_final: 0.8276 (mm)
REVERT: A  307 VAL cc_start: 0.8484 (m) cc_final: 0.8180 (t)
REVERT: A  309 ASN cc_start: 0.7380 (t0) cc_final: 0.6947 (t0)
REVERT: A  343 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6741 (mp0)
REVERT: A  375 GLU cc_start: 0.7602 (pt0) cc_final: 0.7063 (pt0)
REVERT: A  378 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7702 (ttpp)
REVERT: A  385 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7982 (mtpp)
REVERT: A  388 SER cc_start: 0.8577 (t) cc_final: 0.8027 (p)
REVERT: A  389 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8451 (mttm)
REVERT: A  399 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6656 (mt-10)
REVERT: A  403 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7276 (mtm180)
REVERT: A  413 GLU cc_start: 0.7261 (tt0) cc_final: 0.7047 (tt0)
REVERT: A  416 SER cc_start: 0.8944 (m) cc_final: 0.8469 (p)
REVERT: A  427 ILE cc_start: 0.8155 (mt) cc_final: 0.7361 (tt)
REVERT: A  433 GLU cc_start: 0.7679 (mp0) cc_final: 0.7221 (mp0)
REVERT: A  437 TRP cc_start: 0.8194 (m100) cc_final: 0.7240 (m-10)
REVERT: H   13 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7321 (mtmm)
REVERT: H   16 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7094 (mt-10)
REVERT: H   33 PHE cc_start: 0.7602 (m-80) cc_final: 0.7336 (m-10)
REVERT: H   71 VAL cc_start: 0.8665 (p) cc_final: 0.8460 (t)
REVERT: H   99 TYR cc_start: 0.7929 (m-80) cc_final: 0.7644 (m-80)
REVERT: L    7 SER cc_start: 0.8606 (m) cc_final: 0.8222 (p)
REVERT: L   24 ARG cc_start: 0.7137 (mmm160) cc_final: 0.6895 (mmm160)
REVERT: L   42 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7986 (mmmt)
REVERT: L   58 VAL cc_start: 0.8810 (t) cc_final: 0.8518 (p)
REVERT: L  103 LYS cc_start: 0.8030 (tttt) cc_final: 0.7399 (tttt)
REVERT: M   32 TYR cc_start: 0.7736 (m-80) cc_final: 0.7475 (m-10)
REVERT: M   59 TYR cc_start: 0.8520 (m-80) cc_final: 0.8134 (m-80)
REVERT: M   83 LYS cc_start: 0.8354 (mttt) cc_final: 0.8077 (ttmm)
REVERT: M   96 SER cc_start: 0.8324 (m) cc_final: 0.8071 (p)
REVERT: M  100 TYR cc_start: 0.7714 (t80) cc_final: 0.7463 (t80)
REVERT: N   56 SER cc_start: 0.8644 (t) cc_final: 0.8351 (p)
  outliers start: 34
  outliers final: 28
  residues processed: 256
  average time/residue: 0.0753
  time to fit residues: 25.3023
Evaluate side-chains
  266 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   31 PHE
Chi-restraints excluded: chain H residue   53 HIS
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   83 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue  100 PHE
Chi-restraints excluded: chain M residue  102 LEU
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   53 LEU
Chi-restraints excluded: chain N residue   95 LEU
Chi-restraints excluded: chain N residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0020
   chunk 10 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 342 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.107615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.095125 restraints weight = 11996.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.098342 restraints weight = 5123.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.100225 restraints weight = 2623.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.101421 restraints weight = 1553.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.102206 restraints weight = 1041.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.116   6783  Z= 0.125
  Angle     :  0.684  12.713   9226  Z= 0.340
  Chirality :  0.047   0.221    997
  Planarity :  0.004   0.036   1179
  Dihedral  :  4.927  39.081    954
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 24.93 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.28), residues: 841
  helix: -2.31 (2.35), residues: 6
  sheet: -0.71 (0.30), residues: 310
  loop : -2.19 (0.24), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  24 
 TYR   0.030   0.001   TYR N  49 
 PHE   0.020   0.001   PHE A 410 
 TRP   0.037   0.002   TRP H   7 
 HIS   0.003   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6769)
  covalent geometry    : angle       0.66761 ( 9197)
  SS BOND              : bond        0.00731 (   13)
  SS BOND              : angle       2.77724 (   26)
  hydrogen bonds       : bond        0.03084 (  151)
  hydrogen bonds       : angle       5.43197 (  423)
  link_NAG-ASN         : bond        0.00142 (    1)
  link_NAG-ASN         : angle       2.19876 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1194.07 seconds
wall clock time: 21 minutes 14.28 seconds (1274.28 seconds total)