Starting phenix.real_space_refine
on Wed Feb  4 07:16:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dqb_47110/02_2026/9dqb_47110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dqb_47110/02_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_47110/02_2026/9dqb_47110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dqb_47110/02_2026/9dqb_47110.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dqb_47110/02_2026/9dqb_47110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dqb_47110/02_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-2.0-5952/lib/python3.9/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: 2.19, per 1000 atoms: 0.24
  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: 0.79
  Conformation dependent library (CDL) restraints added in 344.7 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: 0.21
  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: 1.18

  Time building geometry restraints manager: 1.05 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: 12304
        2.22 -     4.44: 238
        4.44 -     6.65: 49
        6.65 -     8.87: 9
        8.87 -    11.09: 5
  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 -    18.96: 5076
       18.96 -    37.91: 474
       37.91 -    56.87: 122
       56.87 -    75.82: 20
       75.82 -    94.78: 13
  Dihedral angle restraints: 5705
    sinusoidal: 2369
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" C4' AMP B 601 "
           pdb=" C5' AMP B 601 "
           pdb=" O5' AMP B 601 "
           pdb=" P   AMP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -85.22  -94.78     1      2.00e+01 2.50e-03 2.60e+01
  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
  ... (remaining 5702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1040
       0.047 -    0.094: 265
       0.094 -    0.140: 82
       0.140 -    0.187: 4
       0.187 -    0.234: 4
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" C3' AMP B 601 "
            pdb=" C2' AMP B 601 "
            pdb=" C4' AMP B 601 "
            pdb=" O3' AMP B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.74    0.23 2.00e-01 2.50e+01 1.37e+00
  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
  ... (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:             1.040
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.390
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
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= 0.163
  Angle     :  0.813  11.933  12611  Z= 0.429
  Chirality :  0.046   0.234   1395
  Planarity :  0.004   0.053   1639
  Dihedral  : 16.179  94.780   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
  covalent geometry    : bond        0.00311 ( 9333)
  covalent geometry    : angle       0.80119 (12605)
  hydrogen bonds       : bond        0.18591 (  417)
  hydrogen bonds       : angle       7.27274 ( 1179)
  metal coordination   : bond        0.00861 (    4)
  metal coordination   : angle       6.31129 (    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  : 0.297 
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: 0.0849
  time to fit residues: 41.1166
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  : 0.354 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
D  53 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.171687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.134266 restraints weight = 15251.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139740 restraints weight = 8460.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.143422 restraints weight = 5812.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.145867 restraints weight = 4546.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.147559 restraints weight = 3862.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9337  Z= 0.147
  Angle     :  0.745  11.105  12611  Z= 0.366
  Chirality :  0.048   0.181   1395
  Planarity :  0.005   0.056   1639
  Dihedral  :  7.405  76.545   1280
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.02 %
    Favored  : 72.97 %
  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: -0.29 (0.24), residues: 1141
  helix:  0.19 (0.23), residues: 471
  sheet: -0.09 (0.35), residues: 211
  loop : -0.47 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  59 
 TYR   0.020   0.002   TYR C 144 
 PHE   0.033   0.002   PHE G  64 
 TRP   0.016   0.002   TRP C  53 
 HIS   0.007   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9333)
  covalent geometry    : angle       0.73411 (12605)
  hydrogen bonds       : bond        0.04403 (  417)
  hydrogen bonds       : angle       5.68845 ( 1179)
  metal coordination   : bond        0.00776 (    4)
  metal coordination   : angle       5.91471 (    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: 50
    poor density    : 256
  time to evaluate  : 0.355 
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: 0.6447 (OUTLIER) cc_final: 0.5978 (ptm)
REVERT: C   65 LYS cc_start: 0.8671 (mmtt) cc_final: 0.7738 (mmtm)
REVERT: C   74 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8259 (mtmm)
REVERT: C  104 ARG cc_start: 0.7932 (tpt-90) cc_final: 0.7682 (ttp-110)
REVERT: C  107 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7726 (pt)
REVERT: C  126 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7208 (mt0)
REVERT: C  144 TYR cc_start: 0.8897 (t80) cc_final: 0.8593 (t80)
REVERT: G   27 ILE cc_start: 0.6114 (mp) cc_final: 0.5756 (mp)
REVERT: G   66 PHE cc_start: 0.8815 (t80) cc_final: 0.8413 (t80)
REVERT: G   80 LEU cc_start: 0.8385 (mt) cc_final: 0.8034 (mt)
REVERT: A   45 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7008 (mmmt)
REVERT: A  101 ASN cc_start: 0.8388 (m-40) cc_final: 0.8180 (m110)
REVERT: A  127 ASP cc_start: 0.6957 (m-30) cc_final: 0.6593 (t0)
REVERT: A  206 MET cc_start: 0.3553 (mtt) cc_final: 0.3103 (mtt)
REVERT: A  218 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6006 (tp30)
REVERT: A  221 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7509 (mm-30)
REVERT: A  246 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7521 (mm)
REVERT: A  261 THR cc_start: 0.8366 (p) cc_final: 0.8013 (t)
REVERT: A  322 ASP cc_start: 0.5648 (m-30) cc_final: 0.5345 (m-30)
REVERT: B   43 HIS cc_start: 0.6207 (m90) cc_final: 0.5690 (m90)
REVERT: B   94 ASP cc_start: 0.6613 (t0) cc_final: 0.6186 (m-30)
REVERT: B   96 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8078 (mm)
REVERT: B  197 PHE cc_start: 0.8695 (m-80) cc_final: 0.8248 (m-10)
REVERT: B  249 TYR cc_start: 0.8571 (m-80) cc_final: 0.8314 (m-80)
REVERT: B  261 ASP cc_start: 0.7597 (m-30) cc_final: 0.6997 (m-30)
REVERT: B  368 MET cc_start: 0.5534 (mtp) cc_final: 0.5285 (mtp)
REVERT: B  412 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7516 (tp-100)
REVERT: B  426 LYS cc_start: 0.7736 (pttt) cc_final: 0.7513 (ptpt)
REVERT: B  492 SER cc_start: 0.7812 (t) cc_final: 0.7499 (p)
REVERT: B  529 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7968 (tt)
  outliers start: 50
  outliers final: 24
  residues processed: 289
  average time/residue: 0.0783
  time to fit residues: 31.8407
Evaluate side-chains
  239 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 206
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  107 ILE
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 D residue   61 SER
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   96 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:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 87 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.168745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.132261 restraints weight = 15184.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.137008 restraints weight = 9073.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.140254 restraints weight = 6493.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.142496 restraints weight = 5218.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.143958 restraints weight = 4499.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2955

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= 0.145
  Angle     :  0.715  11.177  12611  Z= 0.347
  Chirality :  0.047   0.170   1395
  Planarity :  0.005   0.054   1639
  Dihedral  :  6.699  61.171   1264
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.22 %
    Favored  : 72.97 %
  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: -0.16 (0.25), residues: 1141
  helix:  0.38 (0.23), residues: 461
  sheet: -0.25 (0.34), residues: 224
  loop : -0.36 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  59 
 TYR   0.019   0.002   TYR C  87 
 PHE   0.028   0.002   PHE B  83 
 TRP   0.022   0.002   TRP B 273 
 HIS   0.004   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9333)
  covalent geometry    : angle       0.70527 (12605)
  hydrogen bonds       : bond        0.03933 (  417)
  hydrogen bonds       : angle       5.36713 ( 1179)
  metal coordination   : bond        0.00757 (    4)
  metal coordination   : angle       5.34841 (    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
  270 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 222
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   12 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7464 (mt-10)
REVERT: C   31 ASN cc_start: 0.6984 (m110) cc_final: 0.6749 (m-40)
REVERT: C   39 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.6074 (mtt)
REVERT: C   65 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8307 (mmtm)
REVERT: C   66 ASP cc_start: 0.8153 (m-30) cc_final: 0.7936 (m-30)
REVERT: C  126 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7229 (mt0)
REVERT: G   66 PHE cc_start: 0.8668 (t80) cc_final: 0.8422 (t80)
REVERT: A   45 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6895 (mmmt)
REVERT: A  127 ASP cc_start: 0.6956 (m-30) cc_final: 0.6620 (t70)
REVERT: A  162 HIS cc_start: 0.7533 (m90) cc_final: 0.7230 (m-70)
REVERT: A  252 ASP cc_start: 0.8176 (p0) cc_final: 0.7215 (m-30)
REVERT: A  261 THR cc_start: 0.8400 (p) cc_final: 0.7935 (t)
REVERT: A  343 LEU cc_start: 0.7427 (mt) cc_final: 0.6982 (mt)
REVERT: B   43 HIS cc_start: 0.6056 (m90) cc_final: 0.5632 (m90)
REVERT: B   94 ASP cc_start: 0.6607 (t0) cc_final: 0.6193 (m-30)
REVERT: B  197 PHE cc_start: 0.8644 (m-80) cc_final: 0.8240 (m-10)
REVERT: B  249 TYR cc_start: 0.8575 (m-80) cc_final: 0.8351 (m-10)
REVERT: B  261 ASP cc_start: 0.7381 (m-30) cc_final: 0.6932 (m-30)
REVERT: B  265 TYR cc_start: 0.8530 (t80) cc_final: 0.8314 (t80)
REVERT: B  269 MET cc_start: 0.8383 (mpp) cc_final: 0.7732 (mpp)
REVERT: B  426 LYS cc_start: 0.7747 (pttt) cc_final: 0.7404 (ptpp)
REVERT: B  475 MET cc_start: 0.6961 (mmt) cc_final: 0.6587 (mmm)
REVERT: B  492 SER cc_start: 0.8114 (t) cc_final: 0.7834 (p)
REVERT: B  529 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8152 (tt)
  outliers start: 48
  outliers final: 30
  residues processed: 258
  average time/residue: 0.0770
  time to fit residues: 28.3773
Evaluate side-chains
  232 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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 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 G residue   26 VAL
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  159 PHE
Chi-restraints excluded: chain A residue  214 CYS
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  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   60 GLN
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  432 CYS
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  526 TYR
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 110 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 88 optimal weight:    9.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
D  53 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
B  56 ASN
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.164373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.124722 restraints weight = 15809.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129994 restraints weight = 8877.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.133529 restraints weight = 6173.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.135868 restraints weight = 4897.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136714 restraints weight = 4203.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9337  Z= 0.158
  Angle     :  0.723   9.385  12611  Z= 0.348
  Chirality :  0.047   0.196   1395
  Planarity :  0.005   0.059   1639
  Dihedral  :  6.364  59.731   1259
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.52 %
    Favored  : 71.97 %
  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: -0.20 (0.25), residues: 1141
  helix:  0.41 (0.24), residues: 457
  sheet: -0.38 (0.34), residues: 225
  loop : -0.37 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 153 
 TYR   0.015   0.002   TYR C 144 
 PHE   0.028   0.002   PHE A  80 
 TRP   0.015   0.002   TRP C  53 
 HIS   0.004   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9333)
  covalent geometry    : angle       0.71419 (12605)
  hydrogen bonds       : bond        0.03788 (  417)
  hydrogen bonds       : angle       5.28347 ( 1179)
  metal coordination   : bond        0.00813 (    4)
  metal coordination   : angle       5.19842 (    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
  263 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 208
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  104 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7842 (mtp85)
REVERT: C  126 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7239 (mt0)
REVERT: C  153 ARG cc_start: 0.8635 (mtm110) cc_final: 0.8429 (ptp-110)
REVERT: D   45 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7983 (mmtm)
REVERT: A   45 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7115 (mmtt)
REVERT: A  127 ASP cc_start: 0.7321 (m-30) cc_final: 0.6688 (t0)
REVERT: A  221 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7570 (mm-30)
REVERT: A  252 ASP cc_start: 0.8355 (p0) cc_final: 0.7488 (m-30)
REVERT: A  261 THR cc_start: 0.8613 (p) cc_final: 0.8290 (t)
REVERT: A  341 GLU cc_start: 0.6202 (tm-30) cc_final: 0.5927 (tm-30)
REVERT: B   43 HIS cc_start: 0.6413 (m90) cc_final: 0.5754 (m-70)
REVERT: B   94 ASP cc_start: 0.6747 (t0) cc_final: 0.6295 (m-30)
REVERT: B  169 THR cc_start: 0.7411 (OUTLIER) cc_final: 0.7209 (m)
REVERT: B  197 PHE cc_start: 0.8848 (m-80) cc_final: 0.8363 (m-10)
REVERT: B  261 ASP cc_start: 0.7939 (m-30) cc_final: 0.7551 (m-30)
REVERT: B  265 TYR cc_start: 0.8525 (t80) cc_final: 0.8291 (t80)
REVERT: B  269 MET cc_start: 0.8596 (mpp) cc_final: 0.7848 (mpp)
REVERT: B  363 MET cc_start: 0.7813 (mmt) cc_final: 0.7605 (mmt)
REVERT: B  412 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7485 (tp-100)
REVERT: B  426 LYS cc_start: 0.8041 (pttt) cc_final: 0.7743 (ptpt)
REVERT: B  475 MET cc_start: 0.7345 (mmt) cc_final: 0.6465 (mmm)
REVERT: B  529 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7951 (tt)
  outliers start: 55
  outliers final: 35
  residues processed: 246
  average time/residue: 0.0833
  time to fit residues: 29.3891
Evaluate side-chains
  226 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
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   43 HIS
Chi-restraints excluded: chain D residue   61 SER
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   60 VAL
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue  121 SER
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 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  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  238 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
D  53 GLN
D  60 ASN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.164145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.124431 restraints weight = 15590.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.129543 restraints weight = 8812.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.133002 restraints weight = 6177.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.135397 restraints weight = 4918.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136778 restraints weight = 4215.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9337  Z= 0.151
  Angle     :  0.705  11.229  12611  Z= 0.341
  Chirality :  0.047   0.242   1395
  Planarity :  0.004   0.061   1639
  Dihedral  :  5.984  54.898   1254
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -0.16 (0.25), residues: 1141
  helix:  0.45 (0.24), residues: 458
  sheet: -0.31 (0.34), residues: 222
  loop : -0.40 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 153 
 TYR   0.017   0.001   TYR G  51 
 PHE   0.028   0.002   PHE A  80 
 TRP   0.018   0.002   TRP C  53 
 HIS   0.008   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9333)
  covalent geometry    : angle       0.69568 (12605)
  hydrogen bonds       : bond        0.03634 (  417)
  hydrogen bonds       : angle       5.24206 ( 1179)
  metal coordination   : bond        0.00783 (    4)
  metal coordination   : angle       5.23516 (    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
  260 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 202
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   11 GLN cc_start: 0.8308 (mp10) cc_final: 0.7822 (mp10)
REVERT: C  104 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.7896 (mtp85)
REVERT: C  122 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7097 (tm-30)
REVERT: C  126 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7226 (mt0)
REVERT: D   45 LYS cc_start: 0.8335 (mmtm) cc_final: 0.7957 (mmtm)
REVERT: G   33 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6774 (tp30)
REVERT: A   45 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7081 (mmtt)
REVERT: A  127 ASP cc_start: 0.7297 (m-30) cc_final: 0.6715 (t0)
REVERT: A  221 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7478 (mm-30)
REVERT: A  252 ASP cc_start: 0.8178 (p0) cc_final: 0.7477 (m-30)
REVERT: A  280 LEU cc_start: 0.6145 (tp) cc_final: 0.5714 (mp)
REVERT: B   43 HIS cc_start: 0.6365 (m90) cc_final: 0.5635 (m-70)
REVERT: B   94 ASP cc_start: 0.6809 (t0) cc_final: 0.6402 (m-30)
REVERT: B  197 PHE cc_start: 0.8808 (m-80) cc_final: 0.8260 (m-10)
REVERT: B  265 TYR cc_start: 0.8494 (t80) cc_final: 0.8264 (t80)
REVERT: B  269 MET cc_start: 0.8613 (mpp) cc_final: 0.7799 (mpp)
REVERT: B  352 MET cc_start: 0.8623 (tpt) cc_final: 0.8307 (tpp)
REVERT: B  412 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7470 (tp-100)
REVERT: B  426 LYS cc_start: 0.8004 (pttt) cc_final: 0.7752 (ptpt)
REVERT: B  475 MET cc_start: 0.7304 (mmt) cc_final: 0.6459 (mmm)
REVERT: B  529 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8037 (tt)
  outliers start: 58
  outliers final: 44
  residues processed: 246
  average time/residue: 0.0760
  time to fit residues: 26.5415
Evaluate side-chains
  238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 189
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
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   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 G residue   26 VAL
Chi-restraints excluded: chain G residue   33 GLU
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  121 SER
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   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  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
D  53 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
A 168 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.168230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.132036 restraints weight = 15214.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.136527 restraints weight = 9257.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.139522 restraints weight = 6715.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.141587 restraints weight = 5420.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.142785 restraints weight = 4710.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9337  Z= 0.137
  Angle     :  0.704  12.987  12611  Z= 0.338
  Chirality :  0.046   0.201   1395
  Planarity :  0.004   0.061   1639
  Dihedral  :  5.859  54.896   1254
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 24.42 %
    Favored  : 69.87 %
  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: -0.13 (0.25), residues: 1141
  helix:  0.51 (0.24), residues: 457
  sheet: -0.41 (0.33), residues: 225
  loop : -0.35 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 176 
 TYR   0.011   0.001   TYR D  51 
 PHE   0.027   0.002   PHE A  80 
 TRP   0.019   0.002   TRP C  53 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9333)
  covalent geometry    : angle       0.69531 (12605)
  hydrogen bonds       : bond        0.03499 (  417)
  hydrogen bonds       : angle       5.20268 ( 1179)
  metal coordination   : bond        0.00721 (    4)
  metal coordination   : angle       5.12351 (    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
  262 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 205
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  122 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: C  126 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7271 (mt0)
REVERT: D   45 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7845 (mmtm)
REVERT: A   45 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7379 (mmtp)
REVERT: A  105 MET cc_start: 0.6598 (ppp) cc_final: 0.6027 (ptp)
REVERT: A  127 ASP cc_start: 0.7061 (m-30) cc_final: 0.6660 (t0)
REVERT: A  252 ASP cc_start: 0.7954 (p0) cc_final: 0.7332 (m-30)
REVERT: B   43 HIS cc_start: 0.6122 (m90) cc_final: 0.5699 (m-70)
REVERT: B   94 ASP cc_start: 0.6748 (t0) cc_final: 0.6419 (m-30)
REVERT: B  197 PHE cc_start: 0.8581 (m-80) cc_final: 0.8130 (m-10)
REVERT: B  261 ASP cc_start: 0.7588 (m-30) cc_final: 0.6725 (m-30)
REVERT: B  269 MET cc_start: 0.8407 (mpp) cc_final: 0.7807 (mpp)
REVERT: B  352 MET cc_start: 0.8665 (tpt) cc_final: 0.8422 (tpp)
REVERT: B  412 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7230 (tp-100)
REVERT: B  475 MET cc_start: 0.6942 (mmt) cc_final: 0.6340 (mmm)
REVERT: B  515 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7789 (p)
REVERT: B  529 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8145 (mp)
  outliers start: 57
  outliers final: 46
  residues processed: 244
  average time/residue: 0.0764
  time to fit residues: 26.6270
Evaluate side-chains
  243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 193
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
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   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   33 GLU
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  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  214 CYS
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 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  175 ILE
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  238 ILE
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0870
   chunk 103 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 88 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
C 111 GLN
D  53 GLN
D  92 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 168 ASN ** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.165095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.125608 restraints weight = 15580.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.130804 restraints weight = 8702.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.134195 restraints weight = 6040.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136496 restraints weight = 4790.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137872 restraints weight = 4109.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9337  Z= 0.139
  Angle     :  0.739  15.060  12611  Z= 0.350
  Chirality :  0.047   0.208   1395
  Planarity :  0.004   0.061   1639
  Dihedral  :  5.832  55.020   1254
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 24.92 %
    Favored  : 69.27 %
  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: -0.08 (0.25), residues: 1141
  helix:  0.52 (0.24), residues: 456
  sheet: -0.35 (0.33), residues: 231
  loop : -0.30 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 153 
 TYR   0.020   0.001   TYR B 265 
 PHE   0.027   0.002   PHE A  80 
 TRP   0.018   0.002   TRP C  53 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9333)
  covalent geometry    : angle       0.73150 (12605)
  hydrogen bonds       : bond        0.03442 (  417)
  hydrogen bonds       : angle       5.18669 ( 1179)
  metal coordination   : bond        0.00786 (    4)
  metal coordination   : angle       4.95988 (    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
  262 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 204
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  104 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7788 (mtp85)
REVERT: C  122 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: C  126 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7170 (mt0)
REVERT: C  144 TYR cc_start: 0.9100 (t80) cc_final: 0.8761 (t80)
REVERT: C  153 ARG cc_start: 0.8485 (mtm110) cc_final: 0.8139 (mmt90)
REVERT: D   45 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7961 (mmtm)
REVERT: D   61 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.6951 (p)
REVERT: A   45 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7438 (mmtp)
REVERT: A  105 MET cc_start: 0.7025 (ppp) cc_final: 0.6469 (ptp)
REVERT: A  127 ASP cc_start: 0.7292 (m-30) cc_final: 0.6686 (t0)
REVERT: A  252 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7466 (m-30)
REVERT: B   59 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7565 (ptp-110)
REVERT: B   94 ASP cc_start: 0.6775 (t0) cc_final: 0.6412 (m-30)
REVERT: B  197 PHE cc_start: 0.8777 (m-80) cc_final: 0.8235 (m-10)
REVERT: B  261 ASP cc_start: 0.8009 (m-30) cc_final: 0.7153 (m-30)
REVERT: B  269 MET cc_start: 0.8660 (mpp) cc_final: 0.7899 (mpp)
REVERT: B  352 MET cc_start: 0.8629 (tpt) cc_final: 0.8348 (tpp)
REVERT: B  363 MET cc_start: 0.7464 (mmt) cc_final: 0.7139 (mmt)
REVERT: B  412 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7533 (tp-100)
REVERT: B  475 MET cc_start: 0.7240 (mmt) cc_final: 0.6705 (mmm)
REVERT: B  515 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7614 (p)
REVERT: B  529 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8012 (mp)
REVERT: B  545 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6613 (tm-30)
  outliers start: 58
  outliers final: 43
  residues processed: 243
  average time/residue: 0.0782
  time to fit residues: 26.8446
Evaluate side-chains
  241 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 192
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   67 ASP
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   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  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  168 ASN
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  145 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
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  527 THR
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:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0670
   chunk 91 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
A 168 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.165430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.125748 restraints weight = 15473.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130878 restraints weight = 8682.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.134261 restraints weight = 6068.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136552 restraints weight = 4827.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.138091 restraints weight = 4155.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9337  Z= 0.135
  Angle     :  0.734  14.935  12611  Z= 0.348
  Chirality :  0.047   0.211   1395
  Planarity :  0.004   0.060   1639
  Dihedral  :  5.741  55.410   1254
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 26.23 %
    Favored  : 68.27 %
  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:  0.01 (0.25), residues: 1141
  helix:  0.57 (0.24), residues: 456
  sheet: -0.19 (0.34), residues: 227
  loop : -0.29 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 153 
 TYR   0.019   0.001   TYR B 265 
 PHE   0.027   0.001   PHE A  80 
 TRP   0.021   0.002   TRP C  53 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9333)
  covalent geometry    : angle       0.72656 (12605)
  hydrogen bonds       : bond        0.03479 (  417)
  hydrogen bonds       : angle       5.15176 ( 1179)
  metal coordination   : bond        0.00737 (    4)
  metal coordination   : angle       4.91308 (    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
  257 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 202
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8970 (pp)
REVERT: C  104 ARG cc_start: 0.8269 (ttp-110) cc_final: 0.7730 (mtp85)
REVERT: C  126 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6963 (mt0)
REVERT: C  144 TYR cc_start: 0.9195 (t80) cc_final: 0.8725 (t80)
REVERT: C  153 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8278 (ptp-110)
REVERT: D   45 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7952 (mmtm)
REVERT: D   57 VAL cc_start: 0.7966 (t) cc_final: 0.7622 (p)
REVERT: D   60 ASN cc_start: 0.8096 (t0) cc_final: 0.7820 (t0)
REVERT: A   45 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7333 (mmtt)
REVERT: A  105 MET cc_start: 0.7113 (ppp) cc_final: 0.6547 (ptp)
REVERT: A  127 ASP cc_start: 0.7333 (m-30) cc_final: 0.6723 (t0)
REVERT: A  149 ASN cc_start: 0.7919 (m-40) cc_final: 0.7678 (m110)
REVERT: A  252 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7535 (m-30)
REVERT: A  280 LEU cc_start: 0.6357 (tp) cc_final: 0.5932 (mp)
REVERT: B   94 ASP cc_start: 0.6811 (t0) cc_final: 0.6408 (m-30)
REVERT: B  197 PHE cc_start: 0.8812 (m-80) cc_final: 0.8239 (m-10)
REVERT: B  269 MET cc_start: 0.8737 (mpp) cc_final: 0.7982 (mpp)
REVERT: B  352 MET cc_start: 0.8554 (tpt) cc_final: 0.8261 (tpp)
REVERT: B  363 MET cc_start: 0.7522 (mmt) cc_final: 0.7143 (mmt)
REVERT: B  412 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7602 (tp-100)
REVERT: B  475 MET cc_start: 0.7334 (mmt) cc_final: 0.6464 (mmm)
REVERT: B  515 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.7527 (p)
REVERT: B  529 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7993 (mp)
REVERT: B  545 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6614 (tm-30)
  outliers start: 55
  outliers final: 42
  residues processed: 241
  average time/residue: 0.0875
  time to fit residues: 29.5876
Evaluate side-chains
  241 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 193
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   81 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 G residue   26 VAL
Chi-restraints excluded: chain G residue   36 PHE
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  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 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  156 THR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
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  527 THR
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:    3.9990
   chunk 79 optimal weight:    0.0670
   chunk 100 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0570
   chunk 14 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 76 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 101 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0020
   overall best weight:    0.2044

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.167179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128548 restraints weight = 15550.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.133865 restraints weight = 8602.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.137343 restraints weight = 5929.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.139724 restraints weight = 4666.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.141314 restraints weight = 3976.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9337  Z= 0.126
  Angle     :  0.750  16.027  12611  Z= 0.357
  Chirality :  0.047   0.216   1395
  Planarity :  0.005   0.060   1639
  Dihedral  :  5.754  54.627   1254
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 28.03 %
    Favored  : 67.77 %
  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:  0.02 (0.25), residues: 1141
  helix:  0.58 (0.24), residues: 455
  sheet: -0.18 (0.34), residues: 224
  loop : -0.30 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 153 
 TYR   0.022   0.001   TYR B 265 
 PHE   0.033   0.002   PHE D  66 
 TRP   0.018   0.001   TRP C  53 
 HIS   0.006   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9333)
  covalent geometry    : angle       0.74370 (12605)
  hydrogen bonds       : bond        0.03395 (  417)
  hydrogen bonds       : angle       5.10238 ( 1179)
  metal coordination   : bond        0.00532 (    4)
  metal coordination   : angle       4.33133 (    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
  243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 201
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   98 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6930 (tm-30)
REVERT: C  107 ILE cc_start: 0.8925 (pt) cc_final: 0.8697 (pt)
REVERT: C  144 TYR cc_start: 0.9076 (t80) cc_final: 0.8667 (t80)
REVERT: C  153 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8201 (ptp-110)
REVERT: D   60 ASN cc_start: 0.8059 (t0) cc_final: 0.7690 (t0)
REVERT: G   82 MET cc_start: 0.4070 (mmt) cc_final: 0.3716 (ppp)
REVERT: A  127 ASP cc_start: 0.7090 (m-30) cc_final: 0.6718 (t70)
REVERT: A  149 ASN cc_start: 0.7860 (m-40) cc_final: 0.7648 (m110)
REVERT: A  247 LEU cc_start: 0.8692 (mt) cc_final: 0.8341 (mt)
REVERT: A  252 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7440 (m-30)
REVERT: A  280 LEU cc_start: 0.6310 (tp) cc_final: 0.5970 (mp)
REVERT: B   94 ASP cc_start: 0.6747 (t0) cc_final: 0.6333 (m-30)
REVERT: B  197 PHE cc_start: 0.8734 (m-80) cc_final: 0.8161 (m-10)
REVERT: B  269 MET cc_start: 0.8636 (mpp) cc_final: 0.7925 (mpp)
REVERT: B  363 MET cc_start: 0.7395 (mmt) cc_final: 0.7087 (mmt)
REVERT: B  412 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7522 (tp-100)
REVERT: B  475 MET cc_start: 0.7279 (mmt) cc_final: 0.6456 (mmm)
REVERT: B  515 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7602 (p)
REVERT: B  529 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7986 (mp)
  outliers start: 42
  outliers final: 37
  residues processed: 231
  average time/residue: 0.0907
  time to fit residues: 29.6878
Evaluate side-chains
  233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 193
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  119 LEU
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 G residue   26 VAL
Chi-restraints excluded: chain A residue   22 GLN
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  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  303 CYS
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   88 ASN
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
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  527 THR
Chi-restraints excluded: chain B residue  529 LEU
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:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 75 optimal weight:    0.3980
   chunk 12 optimal weight:    0.1980
   chunk 25 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 111 GLN
A 168 ASN
** 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 = 0.4152 r_free = 0.4152 target = 0.167039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.127786 restraints weight = 15552.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133060 restraints weight = 8663.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136640 restraints weight = 6029.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.138914 restraints weight = 4770.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.140320 restraints weight = 4099.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9337  Z= 0.133
  Angle     :  0.767  16.053  12611  Z= 0.365
  Chirality :  0.048   0.232   1395
  Planarity :  0.005   0.060   1639
  Dihedral  :  5.633  55.909   1250
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.23 %
    Favored  : 67.37 %
  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: -0.00 (0.25), residues: 1141
  helix:  0.57 (0.24), residues: 456
  sheet: -0.05 (0.34), residues: 219
  loop : -0.40 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 153 
 TYR   0.010   0.001   TYR G  21 
 PHE   0.025   0.001   PHE A  80 
 TRP   0.020   0.001   TRP C  53 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9333)
  covalent geometry    : angle       0.76127 (12605)
  hydrogen bonds       : bond        0.03375 (  417)
  hydrogen bonds       : angle       5.06274 ( 1179)
  metal coordination   : bond        0.00628 (    4)
  metal coordination   : angle       4.39611 (    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
  243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 199
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  104 ARG cc_start: 0.8255 (ttp-110) cc_final: 0.7748 (mtp85)
REVERT: C  126 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7029 (mt0)
REVERT: C  144 TYR cc_start: 0.9128 (t80) cc_final: 0.8671 (t80)
REVERT: C  153 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8224 (ptp-110)
REVERT: D   60 ASN cc_start: 0.8149 (t0) cc_final: 0.7699 (t0)
REVERT: G   40 MET cc_start: 0.5164 (mtp) cc_final: 0.4843 (mmt)
REVERT: G   82 MET cc_start: 0.4181 (mmt) cc_final: 0.3863 (ppp)
REVERT: A  105 MET cc_start: 0.6894 (ppp) cc_final: 0.6434 (ptp)
REVERT: A  127 ASP cc_start: 0.7140 (m-30) cc_final: 0.6713 (t70)
REVERT: A  149 ASN cc_start: 0.7912 (m-40) cc_final: 0.7690 (m110)
REVERT: A  252 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7483 (m-30)
REVERT: B   94 ASP cc_start: 0.6687 (t0) cc_final: 0.6320 (m-30)
REVERT: B  197 PHE cc_start: 0.8769 (m-80) cc_final: 0.8238 (m-10)
REVERT: B  262 ASP cc_start: 0.8582 (p0) cc_final: 0.8271 (p0)
REVERT: B  269 MET cc_start: 0.8691 (mpp) cc_final: 0.7971 (mpp)
REVERT: B  363 MET cc_start: 0.7344 (mmt) cc_final: 0.7122 (mmt)
REVERT: B  412 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7601 (tp-100)
REVERT: B  475 MET cc_start: 0.7351 (mmt) cc_final: 0.6648 (mmm)
REVERT: B  529 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mp)
  outliers start: 44
  outliers final: 36
  residues processed: 230
  average time/residue: 0.0862
  time to fit residues: 28.7164
Evaluate side-chains
  229 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 190
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ASP
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 G residue   26 VAL
Chi-restraints excluded: chain A residue   22 GLN
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  159 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  252 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   88 ASN
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  243 TRP
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  526 TYR
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  529 LEU
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:    4.9990
   chunk 92 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** G  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
A 168 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.167123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.128004 restraints weight = 15452.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.133281 restraints weight = 8640.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136818 restraints weight = 5993.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.139249 restraints weight = 4752.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140824 restraints weight = 4061.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9337  Z= 0.137
  Angle     :  0.793  15.602  12611  Z= 0.374
  Chirality :  0.048   0.217   1395
  Planarity :  0.005   0.063   1639
  Dihedral  :  5.597  56.573   1248
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 28.63 %
    Favored  : 67.17 %
  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:  0.03 (0.25), residues: 1141
  helix:  0.58 (0.24), residues: 456
  sheet: -0.01 (0.34), residues: 219
  loop : -0.38 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 153 
 TYR   0.017   0.002   TYR D  91 
 PHE   0.025   0.001   PHE A  80 
 TRP   0.019   0.001   TRP C  53 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9333)
  covalent geometry    : angle       0.77776 (12605)
  hydrogen bonds       : bond        0.03449 (  417)
  hydrogen bonds       : angle       5.12356 ( 1179)
  metal coordination   : bond        0.01828 (    4)
  metal coordination   : angle       7.17519 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1735.99 seconds
wall clock time: 30 minutes 45.12 seconds (1845.12 seconds total)