Starting phenix.real_space_refine
on Wed Aug  5 10:25:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dqb_47110/08_2026/9dqb_47110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dqb_47110/08_2026/9dqb_47110.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dqb_47110/08_2026/9dqb_47110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dqb_47110/08_2026/9dqb_47110.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dqb_47110/08_2026/9dqb_47110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dqb_47110/08_2026/9dqb_47110.map"
  }
  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=   0.000 sd=   0.022
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       1      5.49       5
     S      47      5.16       5
     C    5799      2.51       5
     N    1583      2.21       5
     O    1723      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9154
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1265
          Classifications: {'peptide': 157}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 140}
    Chain: "D"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 627
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "G"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 626
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "A"
      Number of atoms: 2445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2445
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 300}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 4167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4167
          Classifications: {'peptide': 531}
          Link IDs: {'PTRANS': 26, 'TRANS': 504}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 24
          Unusual residues: {' ZN': 1, 'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 1}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6150  SG  CYS B 158      43.948  64.437  57.603  1.00171.91           S
  ATOM   6177  SG  CYS B 161      40.307  64.407  56.922  1.00183.00           S
  ATOM   8292  SG  CYS B 441      41.473  65.337  60.478  1.00181.57           S
  ATOM   8317  SG  CYS B 444      41.823  67.749  57.982  1.00182.37           S

  Time building chain proxies: 1.92, per 1000 atoms: 0.21
  Number of scatterers: 9154
  At special positions: 0
  Unit cell: (84.39, 99.18, 113.97, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      47     16.00
     P       1     15.00
     O    1723      8.00
     N    1583      7.00
     C    5799      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 320.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 441 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 444 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 161 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 158 "
      Number of angles added : 6


  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 7 sheets defined
      44.2% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'C' and resid 2 through 19
    Processing helix  chain 'C' and resid 94 through 98
      removed outlier: 3.552A  pdb=" N   GLU C  98 " --> pdb=" O   SER C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 122
    Processing helix  chain 'C' and resid 131 through 140
    Processing helix  chain 'C' and resid 140 through 155
    Processing helix  chain 'D' and resid 43 through 56
      removed outlier: 4.178A  pdb=" N   LEU D  47 " --> pdb=" O   HIS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 60
      No H-bonds generated for 'chain 'D' and resid 58 through 60'
    Processing helix  chain 'D' and resid 76 through 81
      removed outlier: 3.511A  pdb=" N   LEU D  80 " --> pdb=" O   THR D  76 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 44 through 55
    Processing helix  chain 'G' and resid 76 through 81
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 19 through 36
      removed outlier: 3.647A  pdb=" N   ARG A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU A  25 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   LEU A  28 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 9.211A  pdb=" N   GLU A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ALA A  30 " --> pdb=" O   TRP A  26 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 59
      removed outlier: 3.542A  pdb=" N   GLY A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 103
      removed outlier: 4.748A  pdb=" N   GLU A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   ARG A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 135 through 149
    Processing helix  chain 'A' and resid 215 through 220
    Processing helix  chain 'A' and resid 226 through 234
      removed outlier: 3.847A  pdb=" N   LYS A 234 " --> pdb=" O   LYS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 254
    Processing helix  chain 'A' and resid 258 through 260
      No H-bonds generated for 'chain 'A' and resid 258 through 260'
    Processing helix  chain 'A' and resid 261 through 281
    Processing helix  chain 'A' and resid 283 through 287
    Processing helix  chain 'A' and resid 288 through 289
      No H-bonds generated for 'chain 'A' and resid 288 through 289'
    Processing helix  chain 'A' and resid 290 through 296
      removed outlier: 3.709A  pdb=" N   TYR A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 320
    Processing helix  chain 'B' and resid 8 through 18
      removed outlier: 3.847A  pdb=" N   ALA B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 40
    Processing helix  chain 'B' and resid 54 through 59
      removed outlier: 3.514A  pdb=" N   ASN B  58 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 68
      removed outlier: 3.519A  pdb=" N   VAL B  68 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 81
    Processing helix  chain 'B' and resid 102 through 108
      removed outlier: 3.502A  pdb=" N   GLN B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 133
    Processing helix  chain 'B' and resid 181 through 197
    Processing helix  chain 'B' and resid 218 through 221
    Processing helix  chain 'B' and resid 222 through 229
      removed outlier: 3.599A  pdb=" N   ARG B 227 " --> pdb=" O   GLU B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 247
    Processing helix  chain 'B' and resid 250 through 260
    Processing helix  chain 'B' and resid 260 through 268
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 283 through 290
    Processing helix  chain 'B' and resid 314 through 336
    Processing helix  chain 'B' and resid 348 through 366
    Processing helix  chain 'B' and resid 372 through 381
      removed outlier: 4.032A  pdb=" N   GLY B 381 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 407
    Processing helix  chain 'B' and resid 460 through 467
    Processing helix  chain 'B' and resid 494 through 499
      removed outlier: 4.262A  pdb=" N   THR B 498 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 502
      No H-bonds generated for 'chain 'B' and resid 500 through 502'
    Processing helix  chain 'B' and resid 536 through 539
      removed outlier: 3.510A  pdb=" N   GLY B 539 " --> pdb=" O   GLU B 536 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 536 through 539'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30
      removed outlier: 7.212A  pdb=" N   ASN C  40 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 38
      removed outlier: 4.623A  pdb=" N   ASP D  86 " --> pdb=" O   LYS D  23 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL D  90 " --> pdb=" O   ILE D  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 23
    Processing sheet with id=AA4, first strand: chain 'G' and resid 33 through 34
      removed outlier: 4.075A  pdb=" N   VAL G  26 " --> pdb=" O   ILE G  34 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   LYS G  25 " --> pdb=" O   ILE G  88 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   VAL G  90 " --> pdb=" O   LYS G  25 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   ILE G  27 " --> pdb=" O   VAL G  90 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ARG G  63 " --> pdb=" O   TYR G  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 107 through 111
      removed outlier: 6.025A  pdb=" N   VAL A  39 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 128 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   VAL A 129 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   GLY A 156 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   LEU A 131 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   VAL A 158 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   GLY A 338 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL B 430 " --> pdb=" O   PHE B 417 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   ARG B 414 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   THR B 150 " --> pdb=" O   ARG B 414 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   SER B 139 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU B 111 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   MET B 113 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B  47 " --> pdb=" O   VAL B  22 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177
    Processing sheet with id=AA7, first strand: chain 'B' and resid 488 through 489
      removed outlier: 3.747A  pdb=" N   THR B 488 " --> pdb=" O   ILE B 482 " (cutoff:3.500A)

    417 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3029
        1.34 -     1.46: 1614
        1.46 -     1.58: 4617
        1.58 -     1.70: 1
        1.70 -     1.82: 72
  Bond restraints: 9333
  Sorted by residual:
  bond pdb=" N   VAL A 245 "
       pdb=" CA  VAL A 245 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.45e+00
  bond pdb=" N   LEU A 246 "
       pdb=" CA  LEU A 246 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.55e+00
  bond pdb=" N   LYS A 248 "
       pdb=" CA  LYS A 248 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.20e-02 6.94e+03 5.09e+00
  bond pdb=" N   LYS A  45 "
       pdb=" CA  LYS A  45 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 1.37e-02 5.33e+03 4.68e+00
  bond pdb=" N   LEU B  81 "
       pdb=" CA  LEU B  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.027 1.31e-02 5.83e+03 4.14e+00
  ... (remaining 9328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 12313
        2.22 -     4.44: 232
        4.44 -     6.65: 48
        6.65 -     8.87: 8
        8.87 -    11.09: 4
  Bond angle restraints: 12605
  Sorted by residual:
  angle pdb=" N   LYS A  45 "
        pdb=" CA  LYS A  45 "
        pdb=" C   LYS A  45 "
      ideal   model   delta    sigma   weight residual
     110.41  104.13    6.28 1.23e+00 6.61e-01 2.61e+01
  angle pdb=" N   LEU B  81 "
        pdb=" CA  LEU B  81 "
        pdb=" C   LEU B  81 "
      ideal   model   delta    sigma   weight residual
     113.18  107.04    6.14 1.21e+00 6.83e-01 2.57e+01
  angle pdb=" CA  LYS D  23 "
        pdb=" CB  LYS D  23 "
        pdb=" CG  LYS D  23 "
      ideal   model   delta    sigma   weight residual
     114.10  123.96   -9.86 2.00e+00 2.50e-01 2.43e+01
  angle pdb=" C   TYR B 442 "
        pdb=" N   VAL B 443 "
        pdb=" CA  VAL B 443 "
      ideal   model   delta    sigma   weight residual
     122.77  118.39    4.38 1.05e+00 9.07e-01 1.74e+01
  angle pdb=" CB  MET A 105 "
        pdb=" CG  MET A 105 "
        pdb=" SD  MET A 105 "
      ideal   model   delta    sigma   weight residual
     112.70  123.79  -11.09 3.00e+00 1.11e-01 1.37e+01
  ... (remaining 12600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.96: 5178
       20.96 -    41.91: 419
       41.91 -    62.87: 88
       62.87 -    83.82: 15
       83.82 -   104.78: 5
  Dihedral angle restraints: 5705
    sinusoidal: 2369
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CA  ASN A 326 "
           pdb=" C   ASN A 326 "
           pdb=" N   ASN A 327 "
           pdb=" CA  ASN A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.83  -23.17     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  ARG G  54 "
           pdb=" C   ARG G  54 "
           pdb=" N   GLN G  55 "
           pdb=" CA  GLN G  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.37  -22.63     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  GLU G  79 "
           pdb=" C   GLU G  79 "
           pdb=" N   LEU G  80 "
           pdb=" CA  LEU G  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.73   20.27     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 5702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 960
       0.041 -    0.082: 303
       0.082 -    0.123: 115
       0.123 -    0.164: 13
       0.164 -    0.204: 4
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CA  LEU B  81 "
            pdb=" N   LEU B  81 "
            pdb=" C   LEU B  81 "
            pdb=" CB  LEU B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  VAL A 245 "
            pdb=" N   VAL A 245 "
            pdb=" C   VAL A 245 "
            pdb=" CB  VAL A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  THR B 356 "
            pdb=" CA  THR B 356 "
            pdb=" OG1 THR B 356 "
            pdb=" CG2 THR B 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.92e-01
  ... (remaining 1392 not shown)

  Planarity restraints: 1639
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  43 "    0.026 2.00e-02 2.50e+03   5.27e-02 2.78e+01
        pdb=" C   GLY A  43 "   -0.091 2.00e-02 2.50e+03
        pdb=" O   GLY A  43 "    0.035 2.00e-02 2.50e+03
        pdb=" N   LEU A  44 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  80 "   -0.012 2.00e-02 2.50e+03   2.52e-02 6.33e+00
        pdb=" C   VAL B  80 "    0.043 2.00e-02 2.50e+03
        pdb=" O   VAL B  80 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B  81 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  91 "    0.007 2.00e-02 2.50e+03   1.33e-02 3.53e+00
        pdb=" CG  TYR D  91 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  91 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  91 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  91 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  91 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  91 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  91 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1636 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 727
        2.73 -     3.28: 10276
        3.28 -     3.82: 16343
        3.82 -     4.36: 19461
        4.36 -     4.90: 31654
  Nonbonded interactions: 78461
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 135 "
            pdb=" OG1 THR B 220 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   PRO A  76 "
            pdb=" NE2 GLN A  79 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG1 THR C 135 "
            pdb=" OE1 GLN C 139 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD2 ASP B 309 "
            pdb=" NH1 ARG B 373 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   THR G  41 "
            pdb=" OG1 THR G  41 "
     model   vdw
     2.273 3.040
  ... (remaining 78456 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'D' and (resid 21 through 51 or resid 53 through 97))
  selection = (chain 'G' and (resid 21 through 51 or resid 53 through 97))
}

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:             1.080
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.340
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
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      :  0.003   0.035   9337  Z= 0.161
  Angle     :  0.800  11.933  12611  Z= 0.426
  Chirality :  0.046   0.204   1395
  Planarity :  0.004   0.053   1639
  Dihedral  : 16.192 104.780   3545
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.16 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 24.42 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.10 (0.25), residues: 1141
  helix:  0.21 (0.24), residues: 456
  sheet:  0.08 (0.35), residues: 203
  loop : -0.23 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  70 
 TYR   0.030   0.002   TYR D  91 
 PHE   0.027   0.001   PHE A  80 
 TRP   0.009   0.001   TRP B 217 
 HIS   0.004   0.001   HIS D  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 ( 9333)
  covalent geometry    : angle       0.78839 /  0.43 (12605)
  hydrogen bonds       : bond        0.18591 / 12.99 (  417)
  hydrogen bonds       : angle       7.27274 /  5.20 ( 1179)
  metal coordination   : bond        0.00861 /  0.43 (    4)
  metal coordination   : angle       6.31129 /  3.10 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 334
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 ASN cc_start: 0.5844 (t0) cc_final: 0.5324 (p0)
REVERT: C   39 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.5979 (mtt)
REVERT: C   58 PHE cc_start: 0.7444 (m-80) cc_final: 0.7184 (m-80)
REVERT: C   66 ASP cc_start: 0.8550 (m-30) cc_final: 0.8340 (m-30)
REVERT: C   93 CYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6252 (p)
REVERT: C  104 ARG cc_start: 0.8085 (tpt-90) cc_final: 0.7039 (mtp85)
REVERT: C  120 LEU cc_start: 0.8313 (tp) cc_final: 0.7917 (tp)
REVERT: C  122 GLU cc_start: 0.7649 (tp30) cc_final: 0.7028 (tm-30)
REVERT: C  136 ILE cc_start: 0.8284 (mm) cc_final: 0.7967 (mt)
REVERT: D   23 LYS cc_start: 0.5669 (tppt) cc_final: 0.4801 (tptp)
REVERT: D   59 MET cc_start: 0.8151 (tpp) cc_final: 0.7528 (tpt)
REVERT: D   89 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6496 (mt-10)
REVERT: G   22 ILE cc_start: 0.7803 (mm) cc_final: 0.7577 (mt)
REVERT: G   25 LYS cc_start: 0.8416 (tptp) cc_final: 0.8114 (ttpt)
REVERT: G   80 LEU cc_start: 0.8265 (mt) cc_final: 0.7793 (mt)
REVERT: G   92 GLN cc_start: 0.7947 (mp10) cc_final: 0.7613 (mp10)
REVERT: G   94 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7558 (tm-30)
REVERT: A   31 GLN cc_start: 0.7395 (tp40) cc_final: 0.6833 (mm-40)
REVERT: A   45 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6894 (mmtt)
REVERT: A  127 ASP cc_start: 0.7106 (m-30) cc_final: 0.6562 (t0)
REVERT: A  206 MET cc_start: 0.2877 (mtt) cc_final: 0.1832 (mtt)
REVERT: A  218 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5492 (tp30)
REVERT: A  224 TRP cc_start: 0.5662 (m100) cc_final: 0.5174 (m100)
REVERT: A  280 LEU cc_start: 0.7887 (tp) cc_final: 0.7404 (mp)
REVERT: A  321 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.6024 (tpt170)
REVERT: A  341 GLU cc_start: 0.5627 (mt-10) cc_final: 0.5334 (tm-30)
REVERT: B   43 HIS cc_start: 0.6648 (m90) cc_final: 0.5659 (m90)
REVERT: B   45 ASP cc_start: 0.5902 (m-30) cc_final: 0.5447 (m-30)
REVERT: B   82 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7108 (mt0)
REVERT: B  144 TYR cc_start: 0.8163 (m-80) cc_final: 0.7948 (m-80)
REVERT: B  197 PHE cc_start: 0.8752 (m-80) cc_final: 0.8225 (m-10)
REVERT: B  249 TYR cc_start: 0.8252 (m-80) cc_final: 0.7769 (m-80)
REVERT: B  250 ASP cc_start: 0.8323 (t0) cc_final: 0.7995 (m-30)
REVERT: B  253 LYS cc_start: 0.9204 (mttp) cc_final: 0.8964 (mmtm)
REVERT: B  283 ASP cc_start: 0.7537 (t0) cc_final: 0.7331 (t70)
REVERT: B  284 TRP cc_start: 0.7849 (t-100) cc_final: 0.7636 (t-100)
REVERT: B  316 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7842 (tppt)
REVERT: B  348 ASP cc_start: 0.8713 (m-30) cc_final: 0.8405 (m-30)
REVERT: B  352 MET cc_start: 0.7211 (tpp) cc_final: 0.6913 (tpp)
REVERT: B  363 MET cc_start: 0.8796 (mmm) cc_final: 0.8582 (mmt)
REVERT: B  368 MET cc_start: 0.5948 (mtp) cc_final: 0.5461 (mtp)
REVERT: B  426 LYS cc_start: 0.8081 (pttt) cc_final: 0.7592 (ptpt)
REVERT: B  475 MET cc_start: 0.7186 (tpp) cc_final: 0.6543 (mmt)
REVERT: B  492 SER cc_start: 0.8042 (t) cc_final: 0.7384 (p)
REVERT: B  499 GLU cc_start: 0.8305 (pm20) cc_final: 0.8051 (pm20)
REVERT: B  524 GLN cc_start: 0.8784 (mm110) cc_final: 0.8448 (mm-40)
REVERT: B  528 LEU cc_start: 0.8333 (tt) cc_final: 0.8011 (tt)
REVERT: B  545 GLU cc_start: 0.8149 (tp30) cc_final: 0.7623 (tm-30)
  outliers start: 25
  outliers final: 13
  residues processed: 352
  average time/residue: 0.0979
  time to fit residues: 47.5150
Evaluate side-chains
  248 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 230
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  321 ARG
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  173 CYS
Chi-restraints excluded: chain B residue  258 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 100 optimal weight:    0.0970
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  53 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.172103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134714 restraints weight = 15224.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.140257 restraints weight = 8467.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.143973 restraints weight = 5791.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.146482 restraints weight = 4522.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.148148 restraints weight = 3838.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9337  Z= 0.141
  Angle     :  0.732  11.283  12611  Z= 0.361
  Chirality :  0.048   0.175   1395
  Planarity :  0.005   0.055   1639
  Dihedral  :  7.729 106.997   1280
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.02 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.28 (0.24), residues: 1141
  helix:  0.19 (0.23), residues: 470
  sheet: -0.08 (0.34), residues: 221
  loop : -0.46 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  59 
 TYR   0.021   0.002   TYR C 144 
 PHE   0.035   0.002   PHE G  64 
 TRP   0.016   0.002   TRP C  53 
 HIS   0.005   0.001   HIS D  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 9333)
  covalent geometry    : angle       0.72047 /  0.36 (12605)
  hydrogen bonds       : bond        0.04318 /  2.92 (  417)
  hydrogen bonds       : angle       5.62319 /  3.98 ( 1179)
  metal coordination   : bond        0.00728 /  0.36 (    4)
  metal coordination   : angle       6.02249 /  2.99 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 258
  time to evaluate  : 0.457 
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: C   39 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6007 (ptm)
REVERT: C   65 LYS cc_start: 0.8683 (mmtt) cc_final: 0.7757 (mmtm)
REVERT: C   74 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8288 (mtmm)
REVERT: C  104 ARG cc_start: 0.7914 (tpt-90) cc_final: 0.7700 (ttp-110)
REVERT: C  126 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7218 (mt0)
REVERT: C  144 TYR cc_start: 0.8884 (t80) cc_final: 0.8536 (t80)
REVERT: G   27 ILE cc_start: 0.5967 (mp) cc_final: 0.5505 (mp)
REVERT: G   39 LYS cc_start: 0.6558 (pttt) cc_final: 0.6206 (ptmm)
REVERT: G   40 MET cc_start: 0.6675 (mmm) cc_final: 0.6375 (mtp)
REVERT: G   66 PHE cc_start: 0.8751 (t80) cc_final: 0.8410 (t80)
REVERT: G   80 LEU cc_start: 0.8368 (mt) cc_final: 0.8036 (mt)
REVERT: G   91 TYR cc_start: 0.5504 (t80) cc_final: 0.5056 (t80)
REVERT: A   45 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6978 (mmmt)
REVERT: A  101 ASN cc_start: 0.8405 (m-40) cc_final: 0.8199 (m110)
REVERT: A  127 ASP cc_start: 0.6950 (m-30) cc_final: 0.6595 (t0)
REVERT: A  218 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6008 (tp30)
REVERT: A  221 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7507 (mm-30)
REVERT: A  246 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7480 (mm)
REVERT: A  261 THR cc_start: 0.8326 (p) cc_final: 0.7978 (t)
REVERT: A  280 LEU cc_start: 0.6943 (tp) cc_final: 0.6738 (mp)
REVERT: B   43 HIS cc_start: 0.6241 (m90) cc_final: 0.5675 (m90)
REVERT: B   94 ASP cc_start: 0.6625 (t0) cc_final: 0.6202 (m-30)
REVERT: B  197 PHE cc_start: 0.8685 (m-80) cc_final: 0.8302 (m-10)
REVERT: B  249 TYR cc_start: 0.8573 (m-80) cc_final: 0.8312 (m-10)
REVERT: B  261 ASP cc_start: 0.7567 (m-30) cc_final: 0.6957 (m-30)
REVERT: B  368 MET cc_start: 0.5487 (mtp) cc_final: 0.5245 (mtp)
REVERT: B  412 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7505 (tp-100)
REVERT: B  492 SER cc_start: 0.7822 (t) cc_final: 0.7523 (p)
REVERT: B  529 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7969 (tt)
  outliers start: 48
  outliers final: 23
  residues processed: 289
  average time/residue: 0.0934
  time to fit residues: 38.2756
Evaluate side-chains
  236 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 206
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
G  29 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 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 = 0.4129 r_free = 0.4129 target = 0.165364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126886 restraints weight = 15395.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.131737 restraints weight = 9207.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.134956 restraints weight = 6623.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.137164 restraints weight = 5359.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.138280 restraints weight = 4680.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9337  Z= 0.176
  Angle     :  0.724  11.357  12611  Z= 0.354
  Chirality :  0.047   0.168   1395
  Planarity :  0.005   0.055   1639
  Dihedral  :  7.345 109.508   1264
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 22.02 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.24 (0.25), residues: 1141
  helix:  0.34 (0.23), residues: 461
  sheet: -0.31 (0.34), residues: 225
  loop : -0.41 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 153 
 TYR   0.022   0.002   TYR C  87 
 PHE   0.029   0.002   PHE A  80 
 TRP   0.019   0.002   TRP B 273 
 HIS   0.003   0.001   HIS D  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.18 ( 9333)
  covalent geometry    : angle       0.71302 /  0.35 (12605)
  hydrogen bonds       : bond        0.04023 /  2.73 (  417)
  hydrogen bonds       : angle       5.41712 /  3.81 ( 1179)
  metal coordination   : bond        0.00954 /  0.47 (    4)
  metal coordination   : angle       5.87118 /  2.97 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 217
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 ASN cc_start: 0.7159 (m110) cc_final: 0.6942 (m-40)
REVERT: C   65 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8215 (mmtm)
REVERT: C  126 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7315 (mt0)
REVERT: G   66 PHE cc_start: 0.8658 (t80) cc_final: 0.8426 (t80)
REVERT: G   79 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6952 (tm-30)
REVERT: A   45 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6998 (mmtt)
REVERT: A  127 ASP cc_start: 0.7188 (m-30) cc_final: 0.6730 (t70)
REVERT: A  252 ASP cc_start: 0.8113 (p0) cc_final: 0.7117 (m-30)
REVERT: A  261 THR cc_start: 0.8509 (p) cc_final: 0.8198 (t)
REVERT: A  343 LEU cc_start: 0.7510 (mt) cc_final: 0.7038 (mt)
REVERT: B   43 HIS cc_start: 0.6096 (m90) cc_final: 0.5386 (m-70)
REVERT: B   94 ASP cc_start: 0.6681 (t0) cc_final: 0.6373 (m-30)
REVERT: B  149 THR cc_start: 0.8695 (m) cc_final: 0.8354 (p)
REVERT: B  197 PHE cc_start: 0.8678 (m-80) cc_final: 0.8230 (m-10)
REVERT: B  261 ASP cc_start: 0.7480 (m-30) cc_final: 0.6996 (m-30)
REVERT: B  263 ILE cc_start: 0.8736 (mm) cc_final: 0.8527 (mm)
REVERT: B  269 MET cc_start: 0.8441 (mpp) cc_final: 0.7761 (mpp)
REVERT: B  475 MET cc_start: 0.7007 (mmt) cc_final: 0.6632 (mmm)
REVERT: B  492 SER cc_start: 0.8207 (t) cc_final: 0.7960 (p)
  outliers start: 58
  outliers final: 35
  residues processed: 259
  average time/residue: 0.0947
  time to fit residues: 34.8099
Evaluate side-chains
  233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 195
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue   19 ASP
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   79 GLU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  526 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 110 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   overall best weight:    3.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  53 GLN
D  92 GLN
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 332 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.155702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.115226 restraints weight = 16053.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.119958 restraints weight = 9129.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.123120 restraints weight = 6467.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.125236 restraints weight = 5205.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.126176 restraints weight = 4519.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   9337  Z= 0.302
  Angle     :  0.815  12.562  12611  Z= 0.404
  Chirality :  0.050   0.240   1395
  Planarity :  0.005   0.062   1639
  Dihedral  :  7.264 108.808   1257
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 21.12 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.56 (0.25), residues: 1141
  helix: -0.01 (0.23), residues: 466
  sheet: -0.52 (0.33), residues: 229
  loop : -0.46 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  91 
 TYR   0.017   0.002   TYR B  92 
 PHE   0.034   0.002   PHE A 331 
 TRP   0.015   0.002   TRP C  53 
 HIS   0.010   0.002   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00703 /  0.30 ( 9333)
  covalent geometry    : angle       0.79976 /  0.40 (12605)
  hydrogen bonds       : bond        0.04347 /  2.93 (  417)
  hydrogen bonds       : angle       5.70557 /  3.98 ( 1179)
  metal coordination   : bond        0.01572 /  0.78 (    4)
  metal coordination   : angle       7.28874 /  3.70 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 207
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 ASN cc_start: 0.6953 (m110) cc_final: 0.6609 (m-40)
REVERT: C  126 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7417 (mt0)
REVERT: D   57 VAL cc_start: 0.8251 (t) cc_final: 0.7817 (t)
REVERT: A   45 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7308 (mmmt)
REVERT: A  168 ASN cc_start: 0.8195 (t0) cc_final: 0.7967 (t0)
REVERT: A  221 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7595 (mm-30)
REVERT: A  252 ASP cc_start: 0.8387 (p0) cc_final: 0.7528 (m-30)
REVERT: A  261 THR cc_start: 0.8910 (p) cc_final: 0.8618 (t)
REVERT: B   43 HIS cc_start: 0.6631 (m90) cc_final: 0.5932 (m-70)
REVERT: B   94 ASP cc_start: 0.6796 (t0) cc_final: 0.6494 (m-30)
REVERT: B  138 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7762 (tm-30)
REVERT: B  197 PHE cc_start: 0.9043 (m-80) cc_final: 0.8396 (m-10)
REVERT: B  265 TYR cc_start: 0.8622 (t80) cc_final: 0.8358 (t80)
REVERT: B  269 MET cc_start: 0.8834 (mpp) cc_final: 0.7967 (mpp)
REVERT: B  283 ASP cc_start: 0.7664 (t0) cc_final: 0.7455 (t0)
REVERT: B  363 MET cc_start: 0.7944 (mmt) cc_final: 0.7705 (mmt)
REVERT: B  475 MET cc_start: 0.7717 (mmt) cc_final: 0.7126 (mmt)
REVERT: B  515 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.7829 (p)
REVERT: B  529 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8216 (tt)
  outliers start: 67
  outliers final: 46
  residues processed: 250
  average time/residue: 0.0873
  time to fit residues: 31.3926
Evaluate side-chains
  238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 186
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 ASP
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0070
   chunk 90 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0050
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.5012

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  53 GLN
D  60 ASN
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  60 GLN
B 290 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.161001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.121649 restraints weight = 15623.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.126531 restraints weight = 8720.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.130046 restraints weight = 6124.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.132344 restraints weight = 4860.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.133659 restraints weight = 4174.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   9337  Z= 0.145
  Angle     :  0.725   9.191  12611  Z= 0.354
  Chirality :  0.047   0.226   1395
  Planarity :  0.005   0.063   1639
  Dihedral  :  6.711 107.413   1253
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 23.02 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.24 (0.25), residues: 1141
  helix:  0.33 (0.24), residues: 447
  sheet: -0.41 (0.34), residues: 225
  loop : -0.32 (0.31), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 153 
 TYR   0.011   0.001   TYR C  87 
 PHE   0.029   0.002   PHE A  80 
 TRP   0.010   0.002   TRP B 273 
 HIS   0.008   0.001   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 9333)
  covalent geometry    : angle       0.71669 /  0.35 (12605)
  hydrogen bonds       : bond        0.03781 /  2.53 (  417)
  hydrogen bonds       : angle       5.43630 /  3.78 ( 1179)
  metal coordination   : bond        0.00674 /  0.33 (    4)
  metal coordination   : angle       5.02427 /  2.50 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 206
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 ASN cc_start: 0.6879 (m110) cc_final: 0.6423 (m110)
REVERT: C   81 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8992 (pp)
REVERT: C   98 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6516 (tm-30)
REVERT: C  122 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7190 (tm-30)
REVERT: C  126 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7272 (mt0)
REVERT: D   44 LEU cc_start: 0.7216 (mm) cc_final: 0.7004 (mm)
REVERT: D   61 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7808 (p)
REVERT: G   79 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7077 (tm-30)
REVERT: A   45 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7351 (mmtt)
REVERT: A  127 ASP cc_start: 0.7612 (m-30) cc_final: 0.6853 (t0)
REVERT: A  168 ASN cc_start: 0.8119 (t0) cc_final: 0.7772 (t0)
REVERT: A  252 ASP cc_start: 0.8200 (p0) cc_final: 0.7511 (m-30)
REVERT: A  261 THR cc_start: 0.8845 (p) cc_final: 0.8528 (t)
REVERT: B   59 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7653 (ptp-110)
REVERT: B   94 ASP cc_start: 0.6661 (t0) cc_final: 0.6365 (m-30)
REVERT: B  197 PHE cc_start: 0.8896 (m-80) cc_final: 0.8232 (m-10)
REVERT: B  265 TYR cc_start: 0.8533 (t80) cc_final: 0.8261 (t80)
REVERT: B  269 MET cc_start: 0.8756 (mpp) cc_final: 0.7869 (mpp)
REVERT: B  363 MET cc_start: 0.7917 (mmt) cc_final: 0.7716 (mmt)
REVERT: B  475 MET cc_start: 0.7611 (mmt) cc_final: 0.7072 (mmt)
REVERT: B  515 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.7745 (p)
REVERT: B  529 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8016 (tt)
  outliers start: 58
  outliers final: 43
  residues processed: 250
  average time/residue: 0.0867
  time to fit residues: 31.4632
Evaluate side-chains
  238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 188
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   42 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   66 PHE
Chi-restraints excluded: chain G residue   79 GLU
Chi-restraints excluded: chain G residue   85 GLU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 0 optimal weight:    0.6980
   chunk 49 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  53 GLN
D  60 ASN
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  60 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.161601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.122275 restraints weight = 15640.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.127324 restraints weight = 8715.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.130755 restraints weight = 6086.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.132755 restraints weight = 4843.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134298 restraints weight = 4216.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9337  Z= 0.147
  Angle     :  0.728  14.925  12611  Z= 0.347
  Chirality :  0.046   0.226   1395
  Planarity :  0.005   0.063   1639
  Dihedral  :  6.591 108.855   1253
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 23.32 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.19 (0.25), residues: 1141
  helix:  0.38 (0.24), residues: 447
  sheet: -0.43 (0.33), residues: 226
  loop : -0.28 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 153 
 TYR   0.014   0.002   TYR C 137 
 PHE   0.030   0.002   PHE A  80 
 TRP   0.010   0.001   TRP C  53 
 HIS   0.008   0.001   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 9333)
  covalent geometry    : angle       0.70916 /  0.35 (12605)
  hydrogen bonds       : bond        0.03667 /  2.44 (  417)
  hydrogen bonds       : angle       5.37516 /  3.72 ( 1179)
  metal coordination   : bond        0.01290 /  0.64 (    4)
  metal coordination   : angle       7.49741 /  3.88 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 199
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 ASN cc_start: 0.7022 (m110) cc_final: 0.6657 (m110)
REVERT: C   81 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8994 (pp)
REVERT: C   98 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6590 (tm-30)
REVERT: C  126 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7224 (mt0)
REVERT: D   44 LEU cc_start: 0.7109 (mm) cc_final: 0.6907 (mm)
REVERT: G   31 SER cc_start: 0.6278 (OUTLIER) cc_final: 0.5888 (p)
REVERT: A   45 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7564 (mmtp)
REVERT: A  127 ASP cc_start: 0.7437 (m-30) cc_final: 0.6726 (t70)
REVERT: A  252 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7492 (m-30)
REVERT: A  261 THR cc_start: 0.8805 (p) cc_final: 0.8496 (t)
REVERT: A  280 LEU cc_start: 0.6248 (tp) cc_final: 0.5835 (mp)
REVERT: B   94 ASP cc_start: 0.6674 (t0) cc_final: 0.6379 (m-30)
REVERT: B  138 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7546 (tm-30)
REVERT: B  197 PHE cc_start: 0.8819 (m-80) cc_final: 0.8209 (m-10)
REVERT: B  265 TYR cc_start: 0.8503 (t80) cc_final: 0.8251 (t80)
REVERT: B  269 MET cc_start: 0.8726 (mpp) cc_final: 0.7942 (mpp)
REVERT: B  363 MET cc_start: 0.7878 (mmt) cc_final: 0.7657 (mmt)
REVERT: B  475 MET cc_start: 0.7552 (mmt) cc_final: 0.6552 (mmm)
REVERT: B  483 GLU cc_start: 0.7278 (pm20) cc_final: 0.7066 (pm20)
REVERT: B  515 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.7759 (p)
REVERT: B  529 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8210 (tt)
  outliers start: 60
  outliers final: 43
  residues processed: 245
  average time/residue: 0.0887
  time to fit residues: 31.0545
Evaluate side-chains
  240 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 189
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   42 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  546 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0370
   chunk 15 optimal weight:    9.9990
   chunk 103 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.7060

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  60 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.162510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.123382 restraints weight = 15761.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.128483 restraints weight = 8747.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.131875 restraints weight = 6075.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134086 restraints weight = 4827.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135563 restraints weight = 4172.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9337  Z= 0.140
  Angle     :  0.724  14.934  12611  Z= 0.347
  Chirality :  0.046   0.183   1395
  Planarity :  0.005   0.063   1639
  Dihedral  :  6.554 110.000   1253
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 24.72 %
    Favored  : 70.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.15 (0.25), residues: 1141
  helix:  0.44 (0.24), residues: 447
  sheet: -0.40 (0.33), residues: 226
  loop : -0.30 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 153 
 TYR   0.013   0.001   TYR C 137 
 PHE   0.028   0.002   PHE A  80 
 TRP   0.011   0.001   TRP C  53 
 HIS   0.007   0.001   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 9333)
  covalent geometry    : angle       0.71270 /  0.35 (12605)
  hydrogen bonds       : bond        0.03600 /  2.40 (  417)
  hydrogen bonds       : angle       5.30845 /  3.68 ( 1179)
  metal coordination   : bond        0.01077 /  0.53 (    4)
  metal coordination   : angle       5.82826 /  2.98 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 200
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.6541 (mpp) cc_final: 0.6236 (mpp)
REVERT: C   65 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8420 (mmtm)
REVERT: C   81 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9015 (pp)
REVERT: C   98 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6775 (tm-30)
REVERT: C  122 GLU cc_start: 0.8317 (tt0) cc_final: 0.8112 (tm-30)
REVERT: C  126 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7173 (mt0)
REVERT: C  153 ARG cc_start: 0.8542 (mtm110) cc_final: 0.8152 (mmt90)
REVERT: A   45 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7535 (mmtp)
REVERT: A  127 ASP cc_start: 0.7431 (m-30) cc_final: 0.6707 (t70)
REVERT: A  168 ASN cc_start: 0.8112 (t0) cc_final: 0.7759 (t0)
REVERT: A  252 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7518 (m-30)
REVERT: A  280 LEU cc_start: 0.6255 (tp) cc_final: 0.5873 (mp)
REVERT: B   94 ASP cc_start: 0.6681 (t0) cc_final: 0.6381 (m-30)
REVERT: B  138 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7548 (tm-30)
REVERT: B  197 PHE cc_start: 0.8852 (m-80) cc_final: 0.8248 (m-10)
REVERT: B  265 TYR cc_start: 0.8473 (t80) cc_final: 0.8203 (t80)
REVERT: B  269 MET cc_start: 0.8781 (mpp) cc_final: 0.7959 (mpp)
REVERT: B  363 MET cc_start: 0.7975 (mmt) cc_final: 0.7734 (mmt)
REVERT: B  368 MET cc_start: 0.5486 (mtp) cc_final: 0.5242 (mtt)
REVERT: B  465 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: B  475 MET cc_start: 0.7570 (mmt) cc_final: 0.6520 (mmm)
REVERT: B  515 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.7708 (p)
REVERT: B  529 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8092 (tt)
  outliers start: 51
  outliers final: 41
  residues processed: 239
  average time/residue: 0.0899
  time to fit residues: 30.7621
Evaluate side-chains
  236 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 188
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   42 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  546 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0470
   chunk 69 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  53 GLN
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** 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 = 0.4123 r_free = 0.4123 target = 0.164264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.124894 restraints weight = 15505.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.129972 restraints weight = 8666.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.133379 restraints weight = 6069.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.135719 restraints weight = 4829.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136948 restraints weight = 4153.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9337  Z= 0.131
  Angle     :  0.727  15.196  12611  Z= 0.347
  Chirality :  0.046   0.177   1395
  Planarity :  0.005   0.062   1639
  Dihedral  :  6.490 111.487   1252
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 26.13 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.11 (0.25), residues: 1141
  helix:  0.49 (0.24), residues: 449
  sheet: -0.35 (0.33), residues: 231
  loop : -0.30 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B  59 
 TYR   0.012   0.001   TYR C 137 
 PHE   0.028   0.002   PHE A 331 
 TRP   0.012   0.001   TRP C  53 
 HIS   0.006   0.001   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 9333)
  covalent geometry    : angle       0.71923 /  0.35 (12605)
  hydrogen bonds       : bond        0.03433 /  2.27 (  417)
  hydrogen bonds       : angle       5.23641 /  3.62 ( 1179)
  metal coordination   : bond        0.00864 /  0.43 (    4)
  metal coordination   : angle       5.06227 /  2.55 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 203
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.6505 (mpp) cc_final: 0.6268 (mpp)
REVERT: C   65 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8400 (mmtm)
REVERT: C   81 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8951 (pp)
REVERT: C   98 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6792 (tm-30)
REVERT: C  126 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7159 (mt0)
REVERT: D   60 ASN cc_start: 0.8311 (t0) cc_final: 0.8108 (t0)
REVERT: G   25 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7144 (mtpt)
REVERT: A   45 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7331 (mmtt)
REVERT: A  127 ASP cc_start: 0.7298 (m-30) cc_final: 0.6667 (t70)
REVERT: A  149 ASN cc_start: 0.7891 (m-40) cc_final: 0.7640 (m110)
REVERT: A  168 ASN cc_start: 0.8102 (t0) cc_final: 0.7731 (t0)
REVERT: A  252 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7511 (m-30)
REVERT: A  280 LEU cc_start: 0.6354 (tp) cc_final: 0.5998 (mp)
REVERT: B   28 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7598 (mt)
REVERT: B   94 ASP cc_start: 0.6683 (t0) cc_final: 0.6342 (m-30)
REVERT: B  138 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7601 (tm-30)
REVERT: B  197 PHE cc_start: 0.8802 (m-80) cc_final: 0.8198 (m-10)
REVERT: B  262 ASP cc_start: 0.8631 (p0) cc_final: 0.8375 (p0)
REVERT: B  265 TYR cc_start: 0.8417 (t80) cc_final: 0.8140 (t80)
REVERT: B  269 MET cc_start: 0.8758 (mpp) cc_final: 0.7949 (mpp)
REVERT: B  368 MET cc_start: 0.5362 (mtp) cc_final: 0.5115 (mtt)
REVERT: B  475 MET cc_start: 0.7573 (mmt) cc_final: 0.6568 (mmm)
REVERT: B  515 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7591 (p)
REVERT: B  529 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8052 (mp)
  outliers start: 48
  outliers final: 38
  residues processed: 239
  average time/residue: 0.0945
  time to fit residues: 31.8215
Evaluate side-chains
  238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 192
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   42 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   45 LYS
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  546 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  53 GLN
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 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 = 0.4126 r_free = 0.4126 target = 0.164820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.126376 restraints weight = 15407.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.131305 restraints weight = 8657.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.134620 restraints weight = 6061.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.136833 restraints weight = 4844.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.138261 restraints weight = 4172.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.4463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9337  Z= 0.165
  Angle     :  0.754  15.103  12611  Z= 0.361
  Chirality :  0.047   0.175   1395
  Planarity :  0.005   0.061   1639
  Dihedral  :  6.553 112.175   1252
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 26.43 %
    Favored  : 68.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.15 (0.25), residues: 1141
  helix:  0.42 (0.24), residues: 446
  sheet: -0.38 (0.33), residues: 229
  loop : -0.28 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  59 
 TYR   0.012   0.001   TYR D  51 
 PHE   0.027   0.002   PHE A  80 
 TRP   0.017   0.001   TRP C  53 
 HIS   0.005   0.001   HIS D  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.16 ( 9333)
  covalent geometry    : angle       0.74265 /  0.36 (12605)
  hydrogen bonds       : bond        0.03605 /  2.40 (  417)
  hydrogen bonds       : angle       5.25309 /  3.64 ( 1179)
  metal coordination   : bond        0.01146 /  0.57 (    4)
  metal coordination   : angle       6.12294 /  3.10 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 191
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.6685 (mpp) cc_final: 0.6391 (mpp)
REVERT: C   65 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8397 (mmtm)
REVERT: C   81 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8955 (pp)
REVERT: C   98 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6850 (tm-30)
REVERT: C  126 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7293 (mt0)
REVERT: D   57 VAL cc_start: 0.8024 (t) cc_final: 0.7676 (p)
REVERT: G   25 LYS cc_start: 0.7621 (ttmt) cc_final: 0.7121 (mtpt)
REVERT: A  127 ASP cc_start: 0.7303 (m-30) cc_final: 0.6778 (t70)
REVERT: A  149 ASN cc_start: 0.7813 (m-40) cc_final: 0.7604 (m110)
REVERT: A  252 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7397 (m-30)
REVERT: B   59 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7674 (ptp-110)
REVERT: B   94 ASP cc_start: 0.6656 (t0) cc_final: 0.6410 (m-30)
REVERT: B  197 PHE cc_start: 0.8783 (m-80) cc_final: 0.8237 (m-10)
REVERT: B  265 TYR cc_start: 0.8406 (t80) cc_final: 0.8148 (t80)
REVERT: B  269 MET cc_start: 0.8625 (mpp) cc_final: 0.7977 (mpp)
REVERT: B  465 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7980 (tm-30)
REVERT: B  475 MET cc_start: 0.7459 (mmt) cc_final: 0.6553 (mmm)
REVERT: B  480 VAL cc_start: 0.8914 (p) cc_final: 0.8708 (p)
REVERT: B  515 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7691 (p)
  outliers start: 50
  outliers final: 42
  residues processed: 228
  average time/residue: 0.0903
  time to fit residues: 29.5871
Evaluate side-chains
  234 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 188
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   35 HIS
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   42 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  546 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 70 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0870
   chunk 29 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 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 = 0.4119 r_free = 0.4119 target = 0.164320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125580 restraints weight = 15544.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.130681 restraints weight = 8630.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.134017 restraints weight = 5954.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.136312 restraints weight = 4706.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.137907 restraints weight = 4017.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9337  Z= 0.139
  Angle     :  0.764  15.214  12611  Z= 0.364
  Chirality :  0.047   0.178   1395
  Planarity :  0.005   0.060   1639
  Dihedral  :  6.427 111.462   1248
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 26.73 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.15 (0.25), residues: 1141
  helix:  0.43 (0.24), residues: 449
  sheet: -0.38 (0.33), residues: 232
  loop : -0.29 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 153 
 TYR   0.014   0.001   TYR C 144 
 PHE   0.025   0.002   PHE B  83 
 TRP   0.014   0.001   TRP C  53 
 HIS   0.007   0.001   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 9333)
  covalent geometry    : angle       0.75669 /  0.36 (12605)
  hydrogen bonds       : bond        0.03492 /  2.31 (  417)
  hydrogen bonds       : angle       5.18502 /  3.58 ( 1179)
  metal coordination   : bond        0.00870 /  0.43 (    4)
  metal coordination   : angle       4.79975 /  2.39 (    6)

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 195
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.6497 (mpp) cc_final: 0.6170 (mpp)
REVERT: C   81 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8974 (pp)
REVERT: C   98 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6894 (tm-30)
REVERT: C  126 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7160 (mt0)
REVERT: C  144 TYR cc_start: 0.9107 (t80) cc_final: 0.8700 (t80)
REVERT: C  153 ARG cc_start: 0.8525 (mtm110) cc_final: 0.8138 (mmt90)
REVERT: D   60 ASN cc_start: 0.8034 (t0) cc_final: 0.7698 (t0)
REVERT: G   25 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7158 (mtpt)
REVERT: A  127 ASP cc_start: 0.7348 (m-30) cc_final: 0.6710 (t70)
REVERT: A  149 ASN cc_start: 0.7931 (m-40) cc_final: 0.7690 (m110)
REVERT: A  168 ASN cc_start: 0.8095 (t0) cc_final: 0.7720 (m-40)
REVERT: A  252 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7477 (m-30)
REVERT: A  323 PRO cc_start: 0.8576 (Cg_endo) cc_final: 0.8338 (Cg_exo)
REVERT: B   28 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7248 (mt)
REVERT: B   59 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7429 (ptp-110)
REVERT: B   94 ASP cc_start: 0.6676 (t0) cc_final: 0.6323 (m-30)
REVERT: B  197 PHE cc_start: 0.8828 (m-80) cc_final: 0.8233 (m-10)
REVERT: B  265 TYR cc_start: 0.8402 (t80) cc_final: 0.8125 (t80)
REVERT: B  269 MET cc_start: 0.8781 (mpp) cc_final: 0.8012 (mpp)
REVERT: B  465 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: B  475 MET cc_start: 0.7551 (mmt) cc_final: 0.6529 (mmm)
REVERT: B  480 VAL cc_start: 0.8780 (p) cc_final: 0.8556 (p)
REVERT: B  515 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.7559 (p)
  outliers start: 45
  outliers final: 38
  residues processed: 227
  average time/residue: 0.0900
  time to fit residues: 29.4869
Evaluate side-chains
  235 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   42 THR
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   74 ASN
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  303 CYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  515 SER
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  546 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 92 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 78 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 481 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 = 0.4137 r_free = 0.4137 target = 0.165469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126542 restraints weight = 15404.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.131719 restraints weight = 8605.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.135132 restraints weight = 5963.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.137470 restraints weight = 4720.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138495 restraints weight = 4035.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9337  Z= 0.133
  Angle     :  0.748  14.016  12611  Z= 0.358
  Chirality :  0.046   0.182   1395
  Planarity :  0.005   0.060   1639
  Dihedral  :  6.385 113.220   1248
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 27.13 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.10 (0.25), residues: 1141
  helix:  0.49 (0.24), residues: 448
  sheet: -0.34 (0.34), residues: 231
  loop : -0.30 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 153 
 TYR   0.012   0.001   TYR D  51 
 PHE   0.026   0.002   PHE A 331 
 TRP   0.013   0.001   TRP C  53 
 HIS   0.005   0.001   HIS A 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 9333)
  covalent geometry    : angle       0.74083 /  0.36 (12605)
  hydrogen bonds       : bond        0.03408 /  2.26 (  417)
  hydrogen bonds       : angle       5.10948 /  3.53 ( 1179)
  metal coordination   : bond        0.00809 /  0.40 (    4)
  metal coordination   : angle       4.82384 /  2.40 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1892.66 seconds
wall clock time: 33 minutes 28.11 seconds (2008.11 seconds total)