Starting phenix.real_space_refine
on Tue Mar  3 22:43:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nyb_0541/03_2026/6nyb_0541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nyb_0541/03_2026/6nyb_0541.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nyb_0541/03_2026/6nyb_0541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nyb_0541/03_2026/6nyb_0541.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nyb_0541/03_2026/6nyb_0541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nyb_0541/03_2026/6nyb_0541.map"
  }
  resolution = 4.1
  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=   0.001 sd=   0.007
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: 9
    Type Number    sf(0)   Gaussians
     I       1     10.91       5
     Zn      2      6.06       5
     P       7      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    5583      2.51       5
     N    1527      2.21       5
     O    1668      1.98       5
     F       1      1.80       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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8842
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2819
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2258
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 16, 'TRANS': 272}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1846
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 5, 'TRANS': 223}
    Chain: "D"
      Number of atoms: 1833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1833
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 223}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' ZN': 2, 'AGS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 53
          Unusual residues: {' MG': 1, 'ADP': 1, 'LCJ': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    136  SG  CYS A 248      61.072  29.426  55.042  1.00 69.52           S
  ATOM    161  SG  CYS A 251      62.989  27.854  57.470  1.00 79.60           S
  ATOM    343  SG  CYS A 272      60.523  25.561  55.470  1.00113.58           S
  ATOM    249  SG  CYS A 261      53.756  37.009  46.317  1.00107.92           S
  ATOM    271  SG  CYS A 264      53.994  38.015  49.372  1.00114.35           S
  ATOM    401  SG  CYS A 280      50.374  39.002  48.986  1.00149.39           S

  Time building chain proxies: 2.31, per 1000 atoms: 0.26
  Number of scatterers: 8842
  At special positions: 0
  Unit cell: (111.3, 93.28, 125.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     I       1     52.95
     Zn      2     29.99
     S      52     16.00
     P       7     15.00
     Mg      1     11.99
     F       1      9.00
     O    1668      8.00
     N    1527      7.00
     C    5583      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: 0.74
  Conformation dependent library (CDL) restraints added in 342.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 272 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 248 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 251 "
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 280 "
        pdb="ZN    ZN A 902 " - pdb=" NE2 HIS A 235 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 264 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 261 "
      Number of angles added : 3


  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      60.2% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 491 through 506
      removed outlier: 3.651A  pdb=" N   GLN A 496 " --> pdb=" O   PRO A 492 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 504 " --> pdb=" O   ASN A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 543
    Processing helix  chain 'A' and resid 549 through 570
    Processing helix  chain 'A' and resid 586 through 588
      No H-bonds generated for 'chain 'A' and resid 586 through 588'
    Processing helix  chain 'A' and resid 621 through 627
    Processing helix  chain 'A' and resid 634 through 652
    Processing helix  chain 'A' and resid 662 through 671
    Processing helix  chain 'A' and resid 686 through 697
      removed outlier: 3.548A  pdb=" N   LEU A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   MET A 693 " --> pdb=" O   MET A 689 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 697 " --> pdb=" O   MET A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 704
    Processing helix  chain 'A' and resid 706 through 719
      removed outlier: 3.601A  pdb=" N   ALA A 712 " --> pdb=" O   PRO A 708 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU A 717 " --> pdb=" O   SER A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 726
      removed outlier: 3.763A  pdb=" N   ARG A 726 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 60
    Processing helix  chain 'B' and resid 64 through 66
      No H-bonds generated for 'chain 'B' and resid 64 through 66'
    Processing helix  chain 'B' and resid 104 through 116
      removed outlier: 3.537A  pdb=" N   GLN B 116 " --> pdb=" O   ILE B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 121
    Processing helix  chain 'B' and resid 150 through 159
      removed outlier: 3.529A  pdb=" N   LYS B 156 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 184
      removed outlier: 3.787A  pdb=" N   LYS B 168 " --> pdb=" O   GLN B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 194
      No H-bonds generated for 'chain 'B' and resid 192 through 194'
    Processing helix  chain 'B' and resid 212 through 223
      removed outlier: 3.521A  pdb=" N   ASN B 221 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 222 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.540A  pdb=" N   GLN B 236 " --> pdb=" O   PRO B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 259
    Processing helix  chain 'B' and resid 309 through 320
    Processing helix  chain 'B' and resid 331 through 342
    Processing helix  chain 'B' and resid 351 through 357
      removed outlier: 3.831A  pdb=" N   VAL B 357 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 367
      removed outlier: 3.516A  pdb=" N   ALA B 366 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 380
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 20 through 32
      removed outlier: 3.758A  pdb=" N   THR C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 70
      removed outlier: 3.933A  pdb=" N   ASN C  42 " --> pdb=" O   ASN C  38 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU C  43 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU C  44 " --> pdb=" O   GLU C  40 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   VAL C  52 " --> pdb=" O   TYR C  48 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG C  55 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLU C  70 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 102
      removed outlier: 4.169A  pdb=" N   GLN C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 131
    Processing helix  chain 'C' and resid 137 through 160
      removed outlier: 3.676A  pdb=" N   VAL C 141 " --> pdb=" O   THR C 137 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU C 143 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE C 155 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   MET C 160 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 181
    Processing helix  chain 'C' and resid 184 through 202
      removed outlier: 4.204A  pdb=" N   GLU C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 210
      removed outlier: 3.558A  pdb=" N   SER C 210 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 207 through 210'
    Processing helix  chain 'C' and resid 211 through 229
    Processing helix  chain 'D' and resid 3 through 16
    Processing helix  chain 'D' and resid 19 through 31
      removed outlier: 3.950A  pdb=" N   VAL D  29 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 67
      removed outlier: 3.814A  pdb=" N   LEU D  44 " --> pdb=" O   GLU D  40 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL D  52 " --> pdb=" O   TYR D  48 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG D  55 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLN D  67 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 89
      removed outlier: 4.376A  pdb=" N   MET D  78 " --> pdb=" O   ARG D  74 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA D  79 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU D  81 " --> pdb=" O   GLN D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 104
      removed outlier: 3.932A  pdb=" N   LEU D 100 " --> pdb=" O   ASP D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 133
      removed outlier: 3.784A  pdb=" N   GLU D 131 " --> pdb=" O   ARG D 127 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL D 132 " --> pdb=" O   TYR D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 160
      removed outlier: 4.276A  pdb=" N   ASN D 139 " --> pdb=" O   GLY D 135 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ASP D 144 " --> pdb=" O   SER D 140 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   SER D 145 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS D 147 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA D 152 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLU D 154 " --> pdb=" O   GLN D 150 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   ILE D 155 " --> pdb=" O   ASP D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 181
    Processing helix  chain 'D' and resid 184 through 202
    Processing helix  chain 'D' and resid 212 through 230
      removed outlier: 4.018A  pdb=" N   SER D 230 " --> pdb=" O   THR D 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 240
    Processing sheet with id=AA2, first strand: chain 'A' and resid 458 through 465
      removed outlier: 7.356A  pdb=" N   GLY A 460 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   LYS A 475 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ARG A 462 " --> pdb=" O   LYS A 473 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LYS A 473 " --> pdb=" O   ARG A 462 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 585
    Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 75
      removed outlier: 5.966A  pdb=" N   LYS B  70 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   SER B  86 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL B  82 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLU B 144 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   PHE B 129 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 198

    478 hydrogen bonds defined for protein.
    1398 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: 1.50

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 3024
        1.37 -     1.55: 5889
        1.55 -     1.74: 11
        1.74 -     1.92: 84
        1.92 -     2.11: 2
  Bond restraints: 9010
  Sorted by residual:
  bond pdb=" C4  AGS A 801 "
       pdb=" C5  AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.386  1.469 -0.083 1.00e-02 1.00e+04 6.96e+01
  bond pdb=" C5  AGS A 801 "
       pdb=" C6  AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.33e+01
  bond pdb=" PG  AGS A 801 "
       pdb=" S1G AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.949  2.074 -0.125 2.00e-02 2.50e+03 3.94e+01
  bond pdb=" C18 LCJ B 901 "
       pdb=" N09 LCJ B 901 "
    ideal  model  delta    sigma   weight residual
    1.349  1.458 -0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C4  ADP B 601 "
       pdb=" C5  ADP B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.384  0.106 2.00e-02 2.50e+03 2.80e+01
  ... (remaining 9005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 10198
        2.45 -     4.89: 1861
        4.89 -     7.34: 85
        7.34 -     9.79: 12
        9.79 -    12.24: 1
  Bond angle restraints: 12157
  Sorted by residual:
  angle pdb=" C5  AGS A 801 "
        pdb=" C4  AGS A 801 "
        pdb=" N3  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     126.80  119.45    7.35 7.41e-01 1.82e+00 9.84e+01
  angle pdb=" C4  AGS A 801 "
        pdb=" C5  AGS A 801 "
        pdb=" N7  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     110.73  106.42    4.31 4.52e-01 4.89e+00 9.11e+01
  angle pdb=" C5  AGS A 801 "
        pdb=" N7  AGS A 801 "
        pdb=" C8  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     103.67  107.48   -3.81 4.26e-01 5.51e+00 7.99e+01
  angle pdb=" N1  AGS A 801 "
        pdb=" C2  AGS A 801 "
        pdb=" N3  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     128.80  123.21    5.59 8.41e-01 1.41e+00 4.42e+01
  angle pdb=" C4  AGS A 801 "
        pdb=" N9  AGS A 801 "
        pdb=" C8  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     105.70  108.67   -2.97 4.55e-01 4.83e+00 4.25e+01
  ... (remaining 12152 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.85: 5040
       18.85 -    37.70: 342
       37.70 -    56.56: 96
       56.56 -    75.41: 24
       75.41 -    94.26: 5
  Dihedral angle restraints: 5507
    sinusoidal: 2301
      harmonic: 3206
  Sorted by residual:
  dihedral pdb=" C   ASP A 587 "
           pdb=" N   ASP A 587 "
           pdb=" CA  ASP A 587 "
           pdb=" CB  ASP A 587 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.54   16.94     0      2.50e+00 1.60e-01 4.59e+01
  dihedral pdb=" N   ASP A 587 "
           pdb=" C   ASP A 587 "
           pdb=" CA  ASP A 587 "
           pdb=" CB  ASP A 587 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.29  -15.49     0      2.50e+00 1.60e-01 3.84e+01
  dihedral pdb=" C   ASP B 190 "
           pdb=" N   ASP B 190 "
           pdb=" CA  ASP B 190 "
           pdb=" CB  ASP B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.64   13.04     0      2.50e+00 1.60e-01 2.72e+01
  ... (remaining 5504 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.138: 1209
       0.138 -    0.277: 121
       0.277 -    0.415: 2
       0.415 -    0.554: 1
       0.554 -    0.692: 1
  Chirality restraints: 1334
  Sorted by residual:
  chirality pdb=" CA  ASP A 587 "
            pdb=" N   ASP A 587 "
            pdb=" C   ASP A 587 "
            pdb=" CB  ASP A 587 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.82    0.69 2.00e-01 2.50e+01 1.20e+01
  chirality pdb=" CA  ASP B 190 "
            pdb=" N   ASP B 190 "
            pdb=" C   ASP B 190 "
            pdb=" CB  ASP B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.28e+00
  chirality pdb=" CA  ASP A 576 "
            pdb=" N   ASP A 576 "
            pdb=" C   ASP A 576 "
            pdb=" CB  ASP A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  ... (remaining 1331 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 726 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.21e+00
        pdb=" C   ARG A 726 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG A 726 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER A 727 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 628 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.77e+00
        pdb=" C   GLN A 628 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLN A 628 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 629 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D 104 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" C   HIS D 104 "    0.040 2.00e-02 2.50e+03
        pdb=" O   HIS D 104 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU D 105 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.65: 89
        2.65 -     3.23: 7940
        3.23 -     3.80: 13875
        3.80 -     4.38: 18945
        4.38 -     4.96: 31445
  Nonbonded interactions: 72294
  Sorted by model distance:
  nonbonded pdb=" O2B ADP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.070 2.170
  nonbonded pdb=" O3P SEP A 729 "
            pdb=" NH2 ARG D  56 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   PHE A 468 "
            pdb=" N   ASN A 486 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" NZ  LYS D  88 "
            pdb=" OE2 GLU D  92 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" O   SER A 520 "
            pdb=" O   GLN A 524 "
     model   vdw
     2.367 3.040
  ... (remaining 72289 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 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ 
r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid  \ 
202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ 
h 230))
  selection = chain 'D'
}

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:             0.550
  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:                    0.030
  Process input model:                     10.820
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
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      :  0.018   0.574   9017  Z= 1.097
  Angle     :  1.861  57.150  12160  Z= 1.323
  Chirality :  0.091   0.692   1334
  Planarity :  0.003   0.029   1548
  Dihedral  : 14.523  94.262   3433
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.39 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  :  5.02 %
    Favored  : 91.32 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.02 (0.22), residues: 1077
  helix: -1.43 (0.18), residues: 596
  sheet: -2.52 (0.58), residues: 57
  loop : -2.65 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  83 
 TYR   0.020   0.002   TYR C 179 
 PHE   0.015   0.002   PHE A 250 
 TRP   0.009   0.001   TRP B 247 
 HIS   0.007   0.002   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.01369 ( 9010)
  covalent geometry    : angle       1.75074 (12157)
  hydrogen bonds       : bond        0.21547 (  478)
  hydrogen bonds       : angle       8.30541 ( 1398)
  metal coordination   : bond        0.40281 (    7)
  metal coordination   : angle      40.20144 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 406
  time to evaluate  : 0.364 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  483 LYS cc_start: 0.8456 (tttt) cc_final: 0.8071 (tttm)
REVERT: A  501 GLU cc_start: 0.8098 (tp30) cc_final: 0.7564 (tp30)
REVERT: A  544 ILE cc_start: 0.8968 (pt) cc_final: 0.8048 (mp)
REVERT: A  640 TYR cc_start: 0.8918 (t80) cc_final: 0.8607 (t80)
REVERT: A  698 LYS cc_start: 0.8373 (mmtp) cc_final: 0.8079 (mmmm)
REVERT: A  715 GLU cc_start: 0.8006 (tt0) cc_final: 0.7763 (tp30)
REVERT: A  723 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4904 (pttt)
REVERT: B   63 LEU cc_start: 0.6489 (mt) cc_final: 0.5629 (mp)
REVERT: B  114 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8680 (tt0)
REVERT: B  130 TYR cc_start: 0.9032 (m-80) cc_final: 0.7898 (m-10)
REVERT: B  146 MET cc_start: 0.8515 (mmm) cc_final: 0.8093 (mmm)
REVERT: B  160 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8107 (ptm-80)
REVERT: B  163 GLU cc_start: 0.7441 (tt0) cc_final: 0.6988 (tm-30)
REVERT: B  195 ASN cc_start: 0.8701 (m-40) cc_final: 0.8293 (m-40)
REVERT: B  207 CYS cc_start: 0.9338 (p) cc_final: 0.8575 (t)
REVERT: B  230 MET cc_start: 0.7535 (tpp) cc_final: 0.7270 (mmt)
REVERT: B  253 LEU cc_start: 0.9634 (mt) cc_final: 0.9290 (mm)
REVERT: B  255 GLU cc_start: 0.8018 (tt0) cc_final: 0.7724 (tt0)
REVERT: B  308 MET cc_start: 0.8177 (mmp) cc_final: 0.7733 (mmm)
REVERT: B  333 GLU cc_start: 0.9430 (mp0) cc_final: 0.9068 (mp0)
REVERT: B  337 PHE cc_start: 0.9124 (t80) cc_final: 0.8882 (t80)
REVERT: B  341 CYS cc_start: 0.8925 (m) cc_final: 0.8249 (m)
REVERT: B  342 LEU cc_start: 0.8780 (mt) cc_final: 0.8455 (mt)
REVERT: B  358 HIS cc_start: 0.6902 (t-90) cc_final: 0.6399 (t-90)
REVERT: B  374 TRP cc_start: 0.8372 (t60) cc_final: 0.7923 (t60)
REVERT: C   14 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8250 (tm-30)
REVERT: C   30 THR cc_start: 0.8892 (m) cc_final: 0.8648 (t)
REVERT: C  100 LEU cc_start: 0.8404 (mt) cc_final: 0.7927 (mt)
REVERT: C  149 TYR cc_start: 0.8207 (m-10) cc_final: 0.7838 (m-10)
REVERT: C  194 GLN cc_start: 0.8542 (tt0) cc_final: 0.8223 (tm-30)
REVERT: D  167 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8015 (ttt-90)
  outliers start: 35
  outliers final: 8
  residues processed: 426
  average time/residue: 0.1158
  time to fit residues: 64.8568
Evaluate side-chains
  240 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 231
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 38 optimal weight:    8.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 269 HIS
A 709 GLN
B  87 HIS
B 243 GLN
C   8 GLN
C 173 ASN
** D  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.108010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.081171 restraints weight = 22518.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.083640 restraints weight = 14284.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.085357 restraints weight = 10640.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.086327 restraints weight = 8701.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.087154 restraints weight = 7645.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100   9017  Z= 0.174
  Angle     :  0.696   9.957  12160  Z= 0.358
  Chirality :  0.042   0.198   1334
  Planarity :  0.006   0.121   1548
  Dihedral  :  7.295  91.231   1240
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.62 (0.25), residues: 1077
  helix:  0.64 (0.20), residues: 602
  sheet: -1.83 (0.58), residues: 63
  loop : -1.73 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG B 181 
 TYR   0.017   0.002   TYR D  82 
 PHE   0.022   0.003   PHE B 209 
 TRP   0.016   0.002   TRP A 476 
 HIS   0.014   0.002   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9010)
  covalent geometry    : angle       0.68546 (12157)
  hydrogen bonds       : bond        0.04792 (  478)
  hydrogen bonds       : angle       4.76226 ( 1398)
  metal coordination   : bond        0.03944 (    7)
  metal coordination   : angle       7.87649 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.370 
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: symmetry clash
REVERT: A  484 MET cc_start: 0.8542 (mtp) cc_final: 0.7977 (mtt)
REVERT: A  501 GLU cc_start: 0.8326 (tp30) cc_final: 0.7916 (tp30)
REVERT: A  505 LEU cc_start: 0.9212 (mt) cc_final: 0.8477 (mt)
REVERT: A  544 ILE cc_start: 0.8374 (pt) cc_final: 0.8132 (mp)
REVERT: A  564 MET cc_start: 0.8471 (tpt) cc_final: 0.8157 (tpp)
REVERT: A  591 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7770 (mtpt)
REVERT: A  608 HIS cc_start: 0.6191 (p90) cc_final: 0.5804 (m90)
REVERT: A  640 TYR cc_start: 0.9230 (t80) cc_final: 0.8869 (t80)
REVERT: A  698 LYS cc_start: 0.8978 (mmtp) cc_final: 0.8707 (mmmm)
REVERT: A  715 GLU cc_start: 0.8066 (tt0) cc_final: 0.7692 (tp30)
REVERT: A  723 LYS cc_start: 0.6971 (ptmt) cc_final: 0.6743 (pttt)
REVERT: B   96 ARG cc_start: 0.7914 (ttt90) cc_final: 0.7598 (ttt180)
REVERT: B  108 ARG cc_start: 0.9080 (ptt180) cc_final: 0.8719 (ptt90)
REVERT: B  114 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8700 (tp30)
REVERT: B  146 MET cc_start: 0.8986 (mmm) cc_final: 0.8107 (mmm)
REVERT: B  160 ARG cc_start: 0.8781 (mtm-85) cc_final: 0.8338 (ptm-80)
REVERT: B  180 LEU cc_start: 0.8951 (mt) cc_final: 0.8532 (mt)
REVERT: B  181 ARG cc_start: 0.8735 (mmp-170) cc_final: 0.8440 (mmp-170)
REVERT: B  195 ASN cc_start: 0.8701 (m-40) cc_final: 0.8303 (m-40)
REVERT: B  197 LEU cc_start: 0.8351 (mm) cc_final: 0.7983 (mt)
REVERT: B  230 MET cc_start: 0.7529 (tpp) cc_final: 0.7284 (mmt)
REVERT: B  233 GLU cc_start: 0.6784 (pp20) cc_final: 0.6028 (pp20)
REVERT: B  242 VAL cc_start: 0.8611 (m) cc_final: 0.8215 (p)
REVERT: B  255 GLU cc_start: 0.8178 (tt0) cc_final: 0.7882 (tt0)
REVERT: B  319 ASN cc_start: 0.9246 (t0) cc_final: 0.8855 (t0)
REVERT: B  342 LEU cc_start: 0.8879 (mt) cc_final: 0.8626 (mt)
REVERT: B  374 TRP cc_start: 0.8406 (t60) cc_final: 0.7999 (t60)
REVERT: C   17 GLU cc_start: 0.7537 (mp0) cc_final: 0.7276 (mp0)
REVERT: C   92 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8247 (mp0)
REVERT: C  100 LEU cc_start: 0.8525 (mt) cc_final: 0.8303 (mt)
REVERT: C  111 ASN cc_start: 0.8415 (t0) cc_final: 0.8161 (t0)
REVERT: C  194 GLN cc_start: 0.8932 (tt0) cc_final: 0.8589 (tm-30)
REVERT: C  198 ASP cc_start: 0.8388 (p0) cc_final: 0.7964 (p0)
REVERT: C  202 GLU cc_start: 0.8293 (mp0) cc_final: 0.8003 (mp0)
REVERT: D   26 MET cc_start: 0.9100 (mmp) cc_final: 0.8743 (mpp)
REVERT: D   59 TRP cc_start: 0.9262 (t60) cc_final: 0.8919 (t60)
REVERT: D  111 ASN cc_start: 0.9124 (t0) cc_final: 0.8775 (t0)
REVERT: D  197 ASP cc_start: 0.8871 (m-30) cc_final: 0.8669 (m-30)
REVERT: D  224 ASN cc_start: 0.9038 (m-40) cc_final: 0.8832 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1066
  time to fit residues: 40.3055
Evaluate side-chains
  208 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 184 HIS
** D  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.102100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.075334 restraints weight = 22082.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.077673 restraints weight = 14062.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.079267 restraints weight = 10443.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.080213 restraints weight = 8552.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080969 restraints weight = 7552.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9017  Z= 0.228
  Angle     :  0.721  13.623  12160  Z= 0.361
  Chirality :  0.043   0.175   1334
  Planarity :  0.005   0.050   1548
  Dihedral  :  7.089  98.030   1240
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.17 (0.25), residues: 1077
  helix:  0.85 (0.21), residues: 617
  sheet: -1.09 (0.60), residues: 51
  loop : -1.43 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 181 
 TYR   0.026   0.002   TYR A 673 
 PHE   0.025   0.003   PHE A 707 
 TRP   0.014   0.002   TRP A 476 
 HIS   0.009   0.002   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 9010)
  covalent geometry    : angle       0.70874 (12157)
  hydrogen bonds       : bond        0.04591 (  478)
  hydrogen bonds       : angle       4.67996 ( 1398)
  metal coordination   : bond        0.02030 (    7)
  metal coordination   : angle       8.41218 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 LEU cc_start: 0.9183 (mt) cc_final: 0.8975 (mt)
REVERT: A  501 GLU cc_start: 0.8335 (tp30) cc_final: 0.7794 (tp30)
REVERT: A  565 ASP cc_start: 0.8742 (t0) cc_final: 0.8453 (t0)
REVERT: A  640 TYR cc_start: 0.9298 (t80) cc_final: 0.8874 (t80)
REVERT: A  698 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8786 (mmmm)
REVERT: A  699 LYS cc_start: 0.8866 (mttp) cc_final: 0.8640 (mmtp)
REVERT: A  715 GLU cc_start: 0.8138 (tt0) cc_final: 0.7798 (tp30)
REVERT: A  723 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7244 (pttt)
REVERT: B  112 ILE cc_start: 0.9093 (tt) cc_final: 0.8588 (tp)
REVERT: B  129 PHE cc_start: 0.7522 (t80) cc_final: 0.7269 (t80)
REVERT: B  130 TYR cc_start: 0.8439 (m-10) cc_final: 0.8132 (m-10)
REVERT: B  146 MET cc_start: 0.9074 (mmm) cc_final: 0.8432 (mmm)
REVERT: B  181 ARG cc_start: 0.8393 (mmp-170) cc_final: 0.8146 (mmm160)
REVERT: B  195 ASN cc_start: 0.8662 (m-40) cc_final: 0.8030 (m-40)
REVERT: B  197 LEU cc_start: 0.8304 (mm) cc_final: 0.7830 (mm)
REVERT: B  233 GLU cc_start: 0.7130 (pp20) cc_final: 0.6555 (pp20)
REVERT: B  242 VAL cc_start: 0.8728 (m) cc_final: 0.7357 (m)
REVERT: B  249 MET cc_start: 0.9251 (tmm) cc_final: 0.8995 (tmm)
REVERT: B  255 GLU cc_start: 0.8218 (tt0) cc_final: 0.7984 (tt0)
REVERT: B  319 ASN cc_start: 0.9280 (t0) cc_final: 0.8828 (t0)
REVERT: B  337 PHE cc_start: 0.9281 (t80) cc_final: 0.8880 (t80)
REVERT: B  341 CYS cc_start: 0.8566 (m) cc_final: 0.8107 (m)
REVERT: B  342 LEU cc_start: 0.8623 (mt) cc_final: 0.8313 (mt)
REVERT: B  374 TRP cc_start: 0.8531 (t60) cc_final: 0.8226 (t60)
REVERT: C   17 GLU cc_start: 0.7668 (mp0) cc_final: 0.7128 (mp0)
REVERT: C   74 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7508 (ptt180)
REVERT: C  100 LEU cc_start: 0.8473 (mt) cc_final: 0.8264 (mt)
REVERT: C  194 GLN cc_start: 0.8971 (tt0) cc_final: 0.8502 (tm-30)
REVERT: C  198 ASP cc_start: 0.8234 (p0) cc_final: 0.7822 (p0)
REVERT: C  202 GLU cc_start: 0.8486 (mp0) cc_final: 0.8183 (mp0)
REVERT: C  218 MET cc_start: 0.9247 (mmm) cc_final: 0.8946 (tpp)
REVERT: C  224 ASN cc_start: 0.9557 (m-40) cc_final: 0.9356 (m-40)
REVERT: D   26 MET cc_start: 0.9195 (mmp) cc_final: 0.8874 (mpp)
REVERT: D   59 TRP cc_start: 0.9315 (t60) cc_final: 0.8950 (t60)
REVERT: D  111 ASN cc_start: 0.9046 (t0) cc_final: 0.8775 (t0)
REVERT: D  224 ASN cc_start: 0.9029 (m-40) cc_final: 0.8815 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.0849
  time to fit residues: 29.0877
Evaluate side-chains
  179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 70 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 62 optimal weight:   30.0000
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 512 ASN
D  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.104021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.077310 restraints weight = 23110.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.079906 restraints weight = 13719.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.081703 restraints weight = 9839.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.082759 restraints weight = 7870.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.083600 restraints weight = 6889.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.5043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9017  Z= 0.135
  Angle     :  0.630  10.946  12160  Z= 0.313
  Chirality :  0.041   0.171   1334
  Planarity :  0.004   0.038   1548
  Dihedral  :  6.891 100.638   1240
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.35 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.18 (0.26), residues: 1077
  helix:  1.16 (0.21), residues: 614
  sheet: -1.00 (0.60), residues: 59
  loop : -1.32 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 181 
 TYR   0.018   0.002   TYR D 178 
 PHE   0.025   0.002   PHE D 174 
 TRP   0.018   0.002   TRP B 247 
 HIS   0.005   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9010)
  covalent geometry    : angle       0.62314 (12157)
  hydrogen bonds       : bond        0.03951 (  478)
  hydrogen bonds       : angle       4.32444 ( 1398)
  metal coordination   : bond        0.01726 (    7)
  metal coordination   : angle       6.07667 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  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: A  501 GLU cc_start: 0.8272 (tp30) cc_final: 0.7722 (tp30)
REVERT: A  544 ILE cc_start: 0.8715 (pt) cc_final: 0.7683 (tt)
REVERT: A  565 ASP cc_start: 0.8556 (t0) cc_final: 0.8263 (t0)
REVERT: A  608 HIS cc_start: 0.5941 (p90) cc_final: 0.5703 (m170)
REVERT: A  640 TYR cc_start: 0.9231 (t80) cc_final: 0.8713 (t80)
REVERT: A  698 LYS cc_start: 0.9071 (mmtp) cc_final: 0.8632 (mmmm)
REVERT: A  715 GLU cc_start: 0.8054 (tt0) cc_final: 0.7771 (tp30)
REVERT: A  723 LYS cc_start: 0.7493 (ptmt) cc_final: 0.7234 (pttt)
REVERT: B   94 MET cc_start: 0.4386 (pmm) cc_final: 0.3994 (pmm)
REVERT: B  129 PHE cc_start: 0.7263 (t80) cc_final: 0.6882 (t80)
REVERT: B  133 PHE cc_start: 0.8162 (t80) cc_final: 0.7891 (t80)
REVERT: B  146 MET cc_start: 0.8932 (mmm) cc_final: 0.8314 (mmm)
REVERT: B  180 LEU cc_start: 0.9131 (tp) cc_final: 0.8359 (tp)
REVERT: B  195 ASN cc_start: 0.8671 (m-40) cc_final: 0.8444 (m-40)
REVERT: B  207 CYS cc_start: 0.8818 (p) cc_final: 0.8240 (t)
REVERT: B  209 PHE cc_start: 0.9221 (p90) cc_final: 0.9000 (p90)
REVERT: B  233 GLU cc_start: 0.7018 (pp20) cc_final: 0.6245 (pp20)
REVERT: B  249 MET cc_start: 0.9156 (tmm) cc_final: 0.8929 (tmm)
REVERT: B  256 MET cc_start: 0.8826 (mtm) cc_final: 0.8570 (mtm)
REVERT: B  319 ASN cc_start: 0.9246 (t0) cc_final: 0.8771 (t0)
REVERT: B  337 PHE cc_start: 0.9312 (t80) cc_final: 0.9069 (t80)
REVERT: B  341 CYS cc_start: 0.8543 (m) cc_final: 0.8318 (m)
REVERT: B  342 LEU cc_start: 0.8639 (mt) cc_final: 0.8340 (mt)
REVERT: B  374 TRP cc_start: 0.8460 (t60) cc_final: 0.8218 (t60)
REVERT: C   17 GLU cc_start: 0.7587 (mp0) cc_final: 0.7087 (mp0)
REVERT: C   74 ARG cc_start: 0.8040 (ptt180) cc_final: 0.7493 (ptt180)
REVERT: C  100 LEU cc_start: 0.8483 (mt) cc_final: 0.8265 (mt)
REVERT: C  202 GLU cc_start: 0.8320 (mp0) cc_final: 0.8075 (mp0)
REVERT: C  218 MET cc_start: 0.9256 (mmm) cc_final: 0.8946 (mmm)
REVERT: D   26 MET cc_start: 0.9204 (mmp) cc_final: 0.8991 (tpp)
REVERT: D   59 TRP cc_start: 0.9296 (t60) cc_final: 0.8916 (t60)
REVERT: D  111 ASN cc_start: 0.9051 (t0) cc_final: 0.8791 (t0)
REVERT: D  224 ASN cc_start: 0.8986 (m-40) cc_final: 0.8763 (m-40)
  outliers start: 1
  outliers final: 1
  residues processed: 239
  average time/residue: 0.0760
  time to fit residues: 26.1532
Evaluate side-chains
  180 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0070
   chunk 60 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** 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 = 0.3612 r_free = 0.3612 target = 0.104839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.078517 restraints weight = 23701.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.081247 restraints weight = 13804.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.083099 restraints weight = 9784.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.084167 restraints weight = 7835.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.084986 restraints weight = 6803.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.5258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9017  Z= 0.118
  Angle     :  0.603   9.036  12160  Z= 0.299
  Chirality :  0.041   0.178   1334
  Planarity :  0.004   0.068   1548
  Dihedral  :  6.698 103.721   1240
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.26), residues: 1077
  helix:  1.29 (0.21), residues: 615
  sheet: -1.16 (0.58), residues: 69
  loop : -1.30 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 181 
 TYR   0.025   0.002   TYR C 178 
 PHE   0.030   0.002   PHE C 174 
 TRP   0.021   0.001   TRP B 247 
 HIS   0.010   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9010)
  covalent geometry    : angle       0.59911 (12157)
  hydrogen bonds       : bond        0.03698 (  478)
  hydrogen bonds       : angle       4.09636 ( 1398)
  metal coordination   : bond        0.01095 (    7)
  metal coordination   : angle       4.32306 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.308 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 GLU cc_start: 0.8332 (tp30) cc_final: 0.7659 (tp30)
REVERT: A  564 MET cc_start: 0.7863 (tpp) cc_final: 0.7599 (tpp)
REVERT: A  565 ASP cc_start: 0.8458 (t0) cc_final: 0.8136 (t0)
REVERT: A  608 HIS cc_start: 0.6126 (p90) cc_final: 0.5908 (m170)
REVERT: A  640 TYR cc_start: 0.9124 (t80) cc_final: 0.8609 (t80)
REVERT: A  698 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8424 (mmmm)
REVERT: A  703 GLU cc_start: 0.8510 (tt0) cc_final: 0.7899 (tm-30)
REVERT: A  715 GLU cc_start: 0.8076 (tt0) cc_final: 0.7772 (tp30)
REVERT: A  723 LYS cc_start: 0.7523 (ptmt) cc_final: 0.7228 (pttt)
REVERT: B   94 MET cc_start: 0.4613 (pmm) cc_final: 0.4124 (pmm)
REVERT: B  129 PHE cc_start: 0.7242 (t80) cc_final: 0.6633 (t80)
REVERT: B  133 PHE cc_start: 0.8214 (t80) cc_final: 0.7845 (t80)
REVERT: B  146 MET cc_start: 0.8935 (mmm) cc_final: 0.8276 (mmm)
REVERT: B  195 ASN cc_start: 0.8555 (m-40) cc_final: 0.8316 (m-40)
REVERT: B  197 LEU cc_start: 0.8203 (mm) cc_final: 0.7862 (mm)
REVERT: B  207 CYS cc_start: 0.8706 (p) cc_final: 0.8416 (p)
REVERT: B  209 PHE cc_start: 0.9350 (p90) cc_final: 0.9018 (p90)
REVERT: B  233 GLU cc_start: 0.7102 (pp20) cc_final: 0.6348 (pp20)
REVERT: B  242 VAL cc_start: 0.8764 (m) cc_final: 0.8439 (m)
REVERT: B  249 MET cc_start: 0.9139 (tmm) cc_final: 0.8913 (tmm)
REVERT: B  264 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8549 (Cg_endo)
REVERT: B  308 MET cc_start: 0.7006 (ttp) cc_final: 0.6356 (tmm)
REVERT: B  319 ASN cc_start: 0.9228 (t0) cc_final: 0.8710 (t0)
REVERT: B  337 PHE cc_start: 0.9260 (t80) cc_final: 0.8989 (t80)
REVERT: B  374 TRP cc_start: 0.8476 (t60) cc_final: 0.8218 (t60)
REVERT: C   17 GLU cc_start: 0.7617 (mp0) cc_final: 0.7142 (mp0)
REVERT: C   74 ARG cc_start: 0.8108 (ptt180) cc_final: 0.7569 (ptt180)
REVERT: C  194 GLN cc_start: 0.8962 (tt0) cc_final: 0.8541 (tm-30)
REVERT: C  198 ASP cc_start: 0.8136 (p0) cc_final: 0.7763 (p0)
REVERT: C  207 ASN cc_start: 0.9018 (p0) cc_final: 0.8783 (p0)
REVERT: C  218 MET cc_start: 0.9260 (mmm) cc_final: 0.8798 (mmm)
REVERT: C  228 TRP cc_start: 0.8834 (m-10) cc_final: 0.8457 (m-90)
REVERT: D   59 TRP cc_start: 0.9273 (t60) cc_final: 0.8884 (t60)
REVERT: D  111 ASN cc_start: 0.9018 (t0) cc_final: 0.8669 (t0)
REVERT: D  197 ASP cc_start: 0.8893 (m-30) cc_final: 0.8690 (m-30)
REVERT: D  224 ASN cc_start: 0.9011 (m-40) cc_final: 0.8765 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0740
  time to fit residues: 25.6880
Evaluate side-chains
  187 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 66 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.104532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.077885 restraints weight = 23604.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.080467 restraints weight = 13825.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.082232 restraints weight = 9952.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.083306 restraints weight = 8015.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.084105 restraints weight = 7001.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.5451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9017  Z= 0.126
  Angle     :  0.607   9.177  12160  Z= 0.305
  Chirality :  0.040   0.179   1334
  Planarity :  0.004   0.055   1548
  Dihedral  :  6.590 105.496   1240
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.41 (0.26), residues: 1077
  helix:  1.42 (0.21), residues: 615
  sheet: -1.01 (0.61), residues: 64
  loop : -1.35 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 181 
 TYR   0.019   0.002   TYR A 656 
 PHE   0.056   0.002   PHE C 174 
 TRP   0.016   0.001   TRP B 247 
 HIS   0.011   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9010)
  covalent geometry    : angle       0.60063 (12157)
  hydrogen bonds       : bond        0.03642 (  478)
  hydrogen bonds       : angle       4.11188 ( 1398)
  metal coordination   : bond        0.00582 (    7)
  metal coordination   : angle       5.52832 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 LEU cc_start: 0.9244 (mt) cc_final: 0.9035 (mt)
REVERT: A  501 GLU cc_start: 0.8230 (tp30) cc_final: 0.7576 (tp30)
REVERT: A  565 ASP cc_start: 0.8371 (t0) cc_final: 0.8073 (t0)
REVERT: A  640 TYR cc_start: 0.9110 (t80) cc_final: 0.8715 (t80)
REVERT: A  647 TYR cc_start: 0.9355 (t80) cc_final: 0.9056 (t80)
REVERT: A  698 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8594 (mmmm)
REVERT: A  703 GLU cc_start: 0.8563 (tt0) cc_final: 0.7959 (tm-30)
REVERT: A  723 LYS cc_start: 0.7558 (ptmt) cc_final: 0.7242 (pttt)
REVERT: B   94 MET cc_start: 0.4413 (pmm) cc_final: 0.3927 (pmm)
REVERT: B  108 ARG cc_start: 0.9232 (ptt180) cc_final: 0.8909 (ptp90)
REVERT: B  133 PHE cc_start: 0.8134 (t80) cc_final: 0.7818 (t80)
REVERT: B  146 MET cc_start: 0.8942 (mmm) cc_final: 0.8287 (mmm)
REVERT: B  155 LEU cc_start: 0.9705 (tt) cc_final: 0.9446 (mm)
REVERT: B  197 LEU cc_start: 0.8077 (mm) cc_final: 0.7769 (mm)
REVERT: B  209 PHE cc_start: 0.9293 (p90) cc_final: 0.9019 (p90)
REVERT: B  233 GLU cc_start: 0.7082 (pp20) cc_final: 0.6381 (pp20)
REVERT: B  242 VAL cc_start: 0.8774 (m) cc_final: 0.8501 (m)
REVERT: B  249 MET cc_start: 0.9133 (tmm) cc_final: 0.8922 (tmm)
REVERT: B  264 PRO cc_start: 0.8864 (Cg_exo) cc_final: 0.8627 (Cg_endo)
REVERT: B  319 ASN cc_start: 0.9189 (t0) cc_final: 0.8668 (t0)
REVERT: B  337 PHE cc_start: 0.9210 (t80) cc_final: 0.8942 (t80)
REVERT: B  341 CYS cc_start: 0.8412 (m) cc_final: 0.8204 (m)
REVERT: B  374 TRP cc_start: 0.8474 (t60) cc_final: 0.8242 (t60)
REVERT: C    5 GLU cc_start: 0.8709 (pt0) cc_final: 0.8486 (pt0)
REVERT: C   17 GLU cc_start: 0.7628 (mp0) cc_final: 0.7158 (mp0)
REVERT: C   74 ARG cc_start: 0.8067 (ptt180) cc_final: 0.7512 (ptt180)
REVERT: C  194 GLN cc_start: 0.8940 (tt0) cc_final: 0.8504 (tm-30)
REVERT: C  198 ASP cc_start: 0.8033 (p0) cc_final: 0.7619 (p0)
REVERT: C  203 LEU cc_start: 0.9028 (mt) cc_final: 0.8650 (mp)
REVERT: C  207 ASN cc_start: 0.9018 (p0) cc_final: 0.8726 (p0)
REVERT: C  218 MET cc_start: 0.9208 (mmm) cc_final: 0.8755 (mmm)
REVERT: C  224 ASN cc_start: 0.9524 (m-40) cc_final: 0.7903 (m-40)
REVERT: C  228 TRP cc_start: 0.8859 (m-10) cc_final: 0.8417 (m-90)
REVERT: D   59 TRP cc_start: 0.9271 (t60) cc_final: 0.8897 (t60)
REVERT: D  111 ASN cc_start: 0.9009 (t0) cc_final: 0.8647 (t0)
REVERT: D  147 LYS cc_start: 0.9346 (mttt) cc_final: 0.8996 (mppt)
REVERT: D  197 ASP cc_start: 0.8875 (m-30) cc_final: 0.8668 (m-30)
REVERT: D  224 ASN cc_start: 0.8952 (m-40) cc_final: 0.8686 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.0812
  time to fit residues: 28.2741
Evaluate side-chains
  184 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 45 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 HIS
D 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.100226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.073712 restraints weight = 23453.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.076065 restraints weight = 14171.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.077735 restraints weight = 10267.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.078522 restraints weight = 8352.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.079349 restraints weight = 7421.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9017  Z= 0.238
  Angle     :  0.735  13.773  12160  Z= 0.368
  Chirality :  0.044   0.211   1334
  Planarity :  0.005   0.046   1548
  Dihedral  :  7.050 107.593   1240
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.35 (0.26), residues: 1077
  helix:  1.38 (0.21), residues: 608
  sheet: -0.93 (0.59), residues: 61
  loop : -1.35 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 181 
 TYR   0.027   0.002   TYR A 538 
 PHE   0.054   0.002   PHE C 174 
 TRP   0.014   0.002   TRP C 228 
 HIS   0.011   0.002   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 9010)
  covalent geometry    : angle       0.72898 (12157)
  hydrogen bonds       : bond        0.04114 (  478)
  hydrogen bonds       : angle       4.50358 ( 1398)
  metal coordination   : bond        0.02559 (    7)
  metal coordination   : angle       6.06062 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 GLU cc_start: 0.8376 (tp30) cc_final: 0.7965 (tp30)
REVERT: A  505 LEU cc_start: 0.9400 (mt) cc_final: 0.8685 (mt)
REVERT: A  544 ILE cc_start: 0.8739 (pt) cc_final: 0.8387 (tt)
REVERT: A  564 MET cc_start: 0.8325 (tpp) cc_final: 0.7983 (tpp)
REVERT: A  565 ASP cc_start: 0.8700 (t0) cc_final: 0.8403 (t0)
REVERT: A  591 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8123 (mttp)
REVERT: A  640 TYR cc_start: 0.9244 (t80) cc_final: 0.8678 (t80)
REVERT: A  698 LYS cc_start: 0.9164 (mmtp) cc_final: 0.8649 (mmmm)
REVERT: A  703 GLU cc_start: 0.8634 (tt0) cc_final: 0.8411 (tt0)
REVERT: B   94 MET cc_start: 0.4429 (pmm) cc_final: 0.4028 (pmm)
REVERT: B  133 PHE cc_start: 0.8212 (t80) cc_final: 0.7867 (t80)
REVERT: B  146 MET cc_start: 0.9053 (mmm) cc_final: 0.8286 (mmm)
REVERT: B  155 LEU cc_start: 0.9698 (tt) cc_final: 0.9450 (mm)
REVERT: B  195 ASN cc_start: 0.8608 (m110) cc_final: 0.8074 (m-40)
REVERT: B  209 PHE cc_start: 0.9002 (p90) cc_final: 0.8645 (p90)
REVERT: B  233 GLU cc_start: 0.7316 (pp20) cc_final: 0.6593 (pp20)
REVERT: B  242 VAL cc_start: 0.9003 (m) cc_final: 0.8743 (m)
REVERT: B  319 ASN cc_start: 0.9123 (t0) cc_final: 0.8528 (t0)
REVERT: B  337 PHE cc_start: 0.9203 (t80) cc_final: 0.8980 (t80)
REVERT: B  341 CYS cc_start: 0.8333 (m) cc_final: 0.8024 (m)
REVERT: C   17 GLU cc_start: 0.7589 (mp0) cc_final: 0.7067 (mp0)
REVERT: C  111 ASN cc_start: 0.8637 (t0) cc_final: 0.8330 (t0)
REVERT: C  207 ASN cc_start: 0.9047 (p0) cc_final: 0.8661 (p0)
REVERT: D  111 ASN cc_start: 0.9061 (t0) cc_final: 0.8753 (t0)
REVERT: D  224 ASN cc_start: 0.9000 (m-40) cc_final: 0.8791 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0828
  time to fit residues: 25.1230
Evaluate side-chains
  165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 72 optimal weight:    0.0570
   chunk 99 optimal weight:    5.9990
   chunk 62 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.5302

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** 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 = 0.3566 r_free = 0.3566 target = 0.102215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.076068 restraints weight = 23131.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.078570 restraints weight = 13828.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.080074 restraints weight = 9980.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081189 restraints weight = 8165.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.081627 restraints weight = 7154.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.5927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9017  Z= 0.151
  Angle     :  0.662  13.005  12160  Z= 0.328
  Chirality :  0.042   0.271   1334
  Planarity :  0.004   0.044   1548
  Dihedral  :  6.911 108.447   1240
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.53 (0.26), residues: 1077
  helix:  1.56 (0.21), residues: 607
  sheet: -0.94 (0.57), residues: 61
  loop : -1.31 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.027   0.002   TYR C 179 
 PHE   0.052   0.002   PHE C 174 
 TRP   0.029   0.002   TRP B 374 
 HIS   0.018   0.002   HIS D 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9010)
  covalent geometry    : angle       0.65241 (12157)
  hydrogen bonds       : bond        0.03784 (  478)
  hydrogen bonds       : angle       4.26240 ( 1398)
  metal coordination   : bond        0.01848 (    7)
  metal coordination   : angle       7.01121 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 GLU cc_start: 0.8352 (tp30) cc_final: 0.7977 (tp30)
REVERT: A  505 LEU cc_start: 0.9410 (mt) cc_final: 0.8746 (mt)
REVERT: A  544 ILE cc_start: 0.8688 (pt) cc_final: 0.8344 (tt)
REVERT: A  564 MET cc_start: 0.7858 (tpp) cc_final: 0.7647 (tpp)
REVERT: A  591 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8087 (mttp)
REVERT: A  640 TYR cc_start: 0.9210 (t80) cc_final: 0.8626 (t80)
REVERT: A  698 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8506 (mmmm)
REVERT: A  703 GLU cc_start: 0.8642 (tt0) cc_final: 0.8416 (tt0)
REVERT: B   94 MET cc_start: 0.4293 (pmm) cc_final: 0.3944 (pmm)
REVERT: B  108 ARG cc_start: 0.9250 (ptt180) cc_final: 0.8909 (ptp90)
REVERT: B  133 PHE cc_start: 0.8217 (t80) cc_final: 0.7858 (t80)
REVERT: B  146 MET cc_start: 0.9011 (mmm) cc_final: 0.8272 (mmm)
REVERT: B  155 LEU cc_start: 0.9698 (tt) cc_final: 0.9429 (mm)
REVERT: B  195 ASN cc_start: 0.8573 (m110) cc_final: 0.8162 (m-40)
REVERT: B  209 PHE cc_start: 0.8886 (p90) cc_final: 0.8583 (p90)
REVERT: B  233 GLU cc_start: 0.7219 (pp20) cc_final: 0.6467 (pp20)
REVERT: B  247 TRP cc_start: 0.9320 (t-100) cc_final: 0.9071 (t-100)
REVERT: B  249 MET cc_start: 0.9094 (tmm) cc_final: 0.8878 (tmm)
REVERT: B  319 ASN cc_start: 0.9073 (t0) cc_final: 0.8476 (t0)
REVERT: B  337 PHE cc_start: 0.9202 (t80) cc_final: 0.8969 (t80)
REVERT: B  341 CYS cc_start: 0.8360 (m) cc_final: 0.8034 (m)
REVERT: C   17 GLU cc_start: 0.7664 (mp0) cc_final: 0.7134 (mp0)
REVERT: C  111 ASN cc_start: 0.8603 (t0) cc_final: 0.8198 (t0)
REVERT: C  194 GLN cc_start: 0.8969 (tt0) cc_final: 0.8413 (tm-30)
REVERT: C  198 ASP cc_start: 0.7968 (p0) cc_final: 0.7535 (p0)
REVERT: C  207 ASN cc_start: 0.9101 (p0) cc_final: 0.8703 (p0)
REVERT: C  224 ASN cc_start: 0.9350 (m-40) cc_final: 0.7294 (m-40)
REVERT: C  228 TRP cc_start: 0.8886 (m-10) cc_final: 0.8211 (m-90)
REVERT: D   26 MET cc_start: 0.9311 (mmt) cc_final: 0.8734 (mpp)
REVERT: D  111 ASN cc_start: 0.9038 (t0) cc_final: 0.8738 (t0)
REVERT: D  197 ASP cc_start: 0.8964 (m-30) cc_final: 0.8761 (m-30)
REVERT: D  224 ASN cc_start: 0.8998 (m-40) cc_final: 0.8735 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0792
  time to fit residues: 24.2870
Evaluate side-chains
  172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0980
   chunk 58 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 37 optimal weight:    7.9990
   chunk 4 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.102114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.078239 restraints weight = 23576.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.078309 restraints weight = 13892.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.079854 restraints weight = 11022.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.080080 restraints weight = 9243.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.080423 restraints weight = 8387.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.6064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9017  Z= 0.162
  Angle     :  0.674  12.778  12160  Z= 0.334
  Chirality :  0.042   0.175   1334
  Planarity :  0.004   0.042   1548
  Dihedral  :  6.880 110.449   1240
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.58 (0.26), residues: 1077
  helix:  1.58 (0.22), residues: 609
  sheet: -0.93 (0.56), residues: 61
  loop : -1.26 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.030   0.002   TYR D 178 
 PHE   0.039   0.002   PHE A 707 
 TRP   0.039   0.002   TRP B 374 
 HIS   0.018   0.002   HIS D 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9010)
  covalent geometry    : angle       0.66624 (12157)
  hydrogen bonds       : bond        0.03866 (  478)
  hydrogen bonds       : angle       4.35215 ( 1398)
  metal coordination   : bond        0.01564 (    7)
  metal coordination   : angle       6.59069 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 GLU cc_start: 0.8358 (tp30) cc_final: 0.8037 (tp30)
REVERT: A  505 LEU cc_start: 0.9414 (mt) cc_final: 0.8803 (mt)
REVERT: A  517 MET cc_start: 0.7861 (mmt) cc_final: 0.7516 (mmt)
REVERT: A  544 ILE cc_start: 0.8703 (pt) cc_final: 0.8359 (tt)
REVERT: A  591 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8086 (mttp)
REVERT: A  620 MET cc_start: 0.8603 (mtt) cc_final: 0.8150 (mtt)
REVERT: A  640 TYR cc_start: 0.9153 (t80) cc_final: 0.8491 (t80)
REVERT: A  698 LYS cc_start: 0.9083 (mmtp) cc_final: 0.8549 (mmmm)
REVERT: A  703 GLU cc_start: 0.8655 (tt0) cc_final: 0.8421 (tt0)
REVERT: B   94 MET cc_start: 0.4383 (pmm) cc_final: 0.4007 (pmm)
REVERT: B  108 ARG cc_start: 0.9259 (ptt180) cc_final: 0.8922 (ptp90)
REVERT: B  133 PHE cc_start: 0.8106 (t80) cc_final: 0.7780 (t80)
REVERT: B  146 MET cc_start: 0.8985 (mmm) cc_final: 0.8309 (mmm)
REVERT: B  155 LEU cc_start: 0.9658 (tt) cc_final: 0.9428 (mm)
REVERT: B  195 ASN cc_start: 0.8652 (m110) cc_final: 0.8233 (m-40)
REVERT: B  209 PHE cc_start: 0.8690 (p90) cc_final: 0.8459 (p90)
REVERT: B  233 GLU cc_start: 0.7297 (pp20) cc_final: 0.6483 (pp20)
REVERT: B  249 MET cc_start: 0.9054 (tmm) cc_final: 0.8823 (tmm)
REVERT: B  319 ASN cc_start: 0.9042 (t0) cc_final: 0.8446 (t0)
REVERT: B  337 PHE cc_start: 0.9182 (t80) cc_final: 0.8868 (t80)
REVERT: B  341 CYS cc_start: 0.8336 (m) cc_final: 0.8065 (m)
REVERT: B  363 ARG cc_start: 0.8210 (ptt180) cc_final: 0.7998 (ptt180)
REVERT: C   17 GLU cc_start: 0.7601 (mp0) cc_final: 0.7133 (mp0)
REVERT: C  111 ASN cc_start: 0.8588 (t0) cc_final: 0.8184 (t0)
REVERT: C  207 ASN cc_start: 0.9101 (p0) cc_final: 0.8641 (p0)
REVERT: C  218 MET cc_start: 0.9164 (mmm) cc_final: 0.8551 (mmm)
REVERT: C  224 ASN cc_start: 0.9350 (m-40) cc_final: 0.7251 (m-40)
REVERT: C  228 TRP cc_start: 0.8889 (m-10) cc_final: 0.8334 (m-90)
REVERT: D   26 MET cc_start: 0.9284 (mmt) cc_final: 0.8684 (mpp)
REVERT: D   59 TRP cc_start: 0.9248 (t60) cc_final: 0.8919 (t60)
REVERT: D  111 ASN cc_start: 0.9033 (t0) cc_final: 0.8732 (t0)
REVERT: D  224 ASN cc_start: 0.8965 (m-40) cc_final: 0.8691 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0800
  time to fit residues: 24.2887
Evaluate side-chains
  172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 4 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 102 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 HIS
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.102986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.076973 restraints weight = 23414.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.079547 restraints weight = 13782.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081325 restraints weight = 9761.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.082383 restraints weight = 7817.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.083214 restraints weight = 6802.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.6188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9017  Z= 0.120
  Angle     :  0.640  12.144  12160  Z= 0.318
  Chirality :  0.042   0.260   1334
  Planarity :  0.004   0.046   1548
  Dihedral  :  6.703 111.650   1240
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.69 (0.26), residues: 1077
  helix:  1.65 (0.21), residues: 611
  sheet: -0.84 (0.55), residues: 61
  loop : -1.20 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 691 
 TYR   0.031   0.002   TYR C 179 
 PHE   0.049   0.002   PHE C 174 
 TRP   0.035   0.002   TRP B 374 
 HIS   0.014   0.001   HIS D 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9010)
  covalent geometry    : angle       0.63480 (12157)
  hydrogen bonds       : bond        0.03665 (  478)
  hydrogen bonds       : angle       4.11768 ( 1398)
  metal coordination   : bond        0.00790 (    7)
  metal coordination   : angle       5.30420 (    3)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 GLU cc_start: 0.8254 (tp30) cc_final: 0.7959 (tp30)
REVERT: A  505 LEU cc_start: 0.9413 (mt) cc_final: 0.8735 (mt)
REVERT: A  517 MET cc_start: 0.7796 (mmt) cc_final: 0.7486 (mmt)
REVERT: A  544 ILE cc_start: 0.8655 (pt) cc_final: 0.8256 (tt)
REVERT: A  591 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7998 (mttp)
REVERT: A  640 TYR cc_start: 0.9149 (t80) cc_final: 0.8906 (t80)
REVERT: A  698 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8444 (mmmm)
REVERT: A  703 GLU cc_start: 0.8649 (tt0) cc_final: 0.8395 (tt0)
REVERT: B   94 MET cc_start: 0.3951 (pmm) cc_final: 0.3588 (pmm)
REVERT: B  133 PHE cc_start: 0.8102 (t80) cc_final: 0.7641 (t80)
REVERT: B  146 MET cc_start: 0.8942 (mmm) cc_final: 0.8253 (mmm)
REVERT: B  155 LEU cc_start: 0.9660 (tt) cc_final: 0.9432 (mm)
REVERT: B  195 ASN cc_start: 0.8616 (m110) cc_final: 0.8254 (m-40)
REVERT: B  233 GLU cc_start: 0.7204 (pp20) cc_final: 0.6362 (pp20)
REVERT: B  249 MET cc_start: 0.9086 (tmm) cc_final: 0.8882 (tmm)
REVERT: B  319 ASN cc_start: 0.8966 (t0) cc_final: 0.8543 (p0)
REVERT: B  337 PHE cc_start: 0.9200 (t80) cc_final: 0.8897 (t80)
REVERT: C   17 GLU cc_start: 0.7490 (mp0) cc_final: 0.7080 (mp0)
REVERT: C  111 ASN cc_start: 0.8532 (t0) cc_final: 0.8150 (t0)
REVERT: C  179 TYR cc_start: 0.9103 (t80) cc_final: 0.8889 (t80)
REVERT: C  207 ASN cc_start: 0.9128 (p0) cc_final: 0.8626 (p0)
REVERT: C  218 MET cc_start: 0.9202 (mmm) cc_final: 0.8601 (mmm)
REVERT: C  224 ASN cc_start: 0.9257 (m-40) cc_final: 0.7223 (m-40)
REVERT: C  228 TRP cc_start: 0.8715 (m-10) cc_final: 0.8092 (m-90)
REVERT: D   26 MET cc_start: 0.9250 (mmt) cc_final: 0.8755 (mpp)
REVERT: D   59 TRP cc_start: 0.9236 (t60) cc_final: 0.8871 (t60)
REVERT: D  111 ASN cc_start: 0.9004 (t0) cc_final: 0.8698 (t0)
REVERT: D  224 ASN cc_start: 0.8953 (m-40) cc_final: 0.8682 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0728
  time to fit residues: 22.9468
Evaluate side-chains
  180 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:   20.0000
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.102449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.075946 restraints weight = 23414.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.078392 restraints weight = 14170.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.079992 restraints weight = 10340.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.080880 restraints weight = 8460.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081754 restraints weight = 7468.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.6257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9017  Z= 0.136
  Angle     :  0.643  11.273  12160  Z= 0.321
  Chirality :  0.042   0.221   1334
  Planarity :  0.004   0.042   1548
  Dihedral  :  6.700 113.583   1240
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.74 (0.26), residues: 1077
  helix:  1.71 (0.22), residues: 611
  sheet: -0.65 (0.56), residues: 64
  loop : -1.24 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  74 
 TYR   0.024   0.002   TYR C 179 
 PHE   0.028   0.002   PHE B 129 
 TRP   0.033   0.002   TRP B 374 
 HIS   0.013   0.002   HIS D 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9010)
  covalent geometry    : angle       0.63773 (12157)
  hydrogen bonds       : bond        0.03746 (  478)
  hydrogen bonds       : angle       4.15268 ( 1398)
  metal coordination   : bond        0.01142 (    7)
  metal coordination   : angle       5.40545 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1516.72 seconds
wall clock time: 26 minutes 53.38 seconds (1613.38 seconds total)