Starting phenix.real_space_refine
on Fri Sep 11 11:01:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6nyb_0541/09_2026/6nyb_0541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nyb_0541/09_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_0541/09_2026/6nyb_0541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nyb_0541/09_2026/6nyb_0541.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6nyb_0541/09_2026/6nyb_0541.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6nyb_0541/09_2026/6nyb_0541.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nyb_0541/09_2026/6nyb_0541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nyb_0541/09_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-2.2.1-6174/lib/python3.11/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: 2.03, per 1000 atoms: 0.23
  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: 0.90
  Conformation dependent library (CDL) restraints added in 319.8 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: 0.23
  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: 1.26

  Time building geometry restraints manager: 1.12 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: 334
       37.70 -    56.56: 94
       56.56 -    75.41: 23
       75.41 -    94.26: 5
  Dihedral angle restraints: 5496
    sinusoidal: 2290
      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 5493 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:             0.580
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.430
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
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  : 14.408  94.262   3422
  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/Z
  covalent geometry    : bond        0.01369 /  1.03 ( 9010)
  covalent geometry    : angle       1.75074 /  1.31 (12157)
  hydrogen bonds       : bond        0.21547 / 14.02 (  478)
  hydrogen bonds       : angle       8.30541 /  5.79 ( 1398)
  metal coordination   : bond        0.40281 / 20.24 (    7)
  metal coordination   : angle      40.20144 / 22.54 (    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  : 0.354 
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: 0.1119
  time to fit residues: 63.3190
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  : 0.444 
-------------------------------------------------------------------------------
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...
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 = 0.3656 r_free = 0.3656 target = 0.108103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.081184 restraints weight = 22647.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.083688 restraints weight = 14407.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085404 restraints weight = 10704.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.086467 restraints weight = 8725.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.087257 restraints weight = 7662.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9017  Z= 0.176
  Angle     :  0.690  10.832  12160  Z= 0.354
  Chirality :  0.042   0.192   1334
  Planarity :  0.006   0.117   1548
  Dihedral  :  6.943  90.750   1229
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  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: -0.55 (0.25), residues: 1077
  helix:  0.71 (0.21), residues: 599
  sheet: -1.37 (0.63), residues: 53
  loop : -1.79 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG B 181 
 TYR   0.017   0.002   TYR D  82 
 PHE   0.023   0.003   PHE B 209 
 TRP   0.017   0.002   TRP A 476 
 HIS   0.013   0.002   HIS A 269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 ( 9010)
  covalent geometry    : angle       0.67730 /  0.35 (12157)
  hydrogen bonds       : bond        0.04760 /  3.07 (  478)
  hydrogen bonds       : angle       4.75746 /  3.29 ( 1398)
  metal coordination   : bond        0.02901 /  1.64 (    7)
  metal coordination   : angle       8.34263 /  4.48 (    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
  280 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.360 
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  483 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8250 (tttm)
REVERT: A  484 MET cc_start: 0.8532 (mtp) cc_final: 0.7993 (mtt)
REVERT: A  501 GLU cc_start: 0.8314 (tp30) cc_final: 0.7922 (tp30)
REVERT: A  505 LEU cc_start: 0.9208 (mt) cc_final: 0.8509 (mt)
REVERT: A  544 ILE cc_start: 0.8381 (pt) cc_final: 0.8157 (mp)
REVERT: A  564 MET cc_start: 0.8426 (tpt) cc_final: 0.8086 (tpp)
REVERT: A  591 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7773 (mtpt)
REVERT: A  608 HIS cc_start: 0.6127 (p90) cc_final: 0.5776 (m90)
REVERT: A  640 TYR cc_start: 0.9231 (t80) cc_final: 0.8830 (t80)
REVERT: A  698 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8668 (mmmm)
REVERT: A  699 LYS cc_start: 0.8512 (mttp) cc_final: 0.8227 (mmtp)
REVERT: A  715 GLU cc_start: 0.8073 (tt0) cc_final: 0.7658 (tp30)
REVERT: B   96 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7601 (ttt180)
REVERT: B  108 ARG cc_start: 0.9081 (ptt180) cc_final: 0.8713 (ptt90)
REVERT: B  114 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8709 (tp30)
REVERT: B  146 MET cc_start: 0.8976 (mmm) cc_final: 0.8106 (mmm)
REVERT: B  160 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8339 (ptm-80)
REVERT: B  180 LEU cc_start: 0.8997 (mt) cc_final: 0.8519 (mt)
REVERT: B  181 ARG cc_start: 0.8799 (mmp-170) cc_final: 0.8448 (mmp-170)
REVERT: B  195 ASN cc_start: 0.8712 (m-40) cc_final: 0.8321 (m-40)
REVERT: B  197 LEU cc_start: 0.8358 (mm) cc_final: 0.7985 (mt)
REVERT: B  230 MET cc_start: 0.7527 (tpp) cc_final: 0.7288 (mmt)
REVERT: B  233 GLU cc_start: 0.6793 (pp20) cc_final: 0.6050 (pp20)
REVERT: B  242 VAL cc_start: 0.8587 (m) cc_final: 0.8183 (p)
REVERT: B  255 GLU cc_start: 0.8187 (tt0) cc_final: 0.7897 (tt0)
REVERT: B  319 ASN cc_start: 0.9246 (t0) cc_final: 0.8856 (t0)
REVERT: B  342 LEU cc_start: 0.8900 (mt) cc_final: 0.8651 (mt)
REVERT: B  374 TRP cc_start: 0.8348 (t60) cc_final: 0.7988 (t60)
REVERT: C   92 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8248 (mp0)
REVERT: C  100 LEU cc_start: 0.8524 (mt) cc_final: 0.8302 (mt)
REVERT: C  111 ASN cc_start: 0.8419 (t0) cc_final: 0.8173 (t0)
REVERT: C  194 GLN cc_start: 0.8920 (tt0) cc_final: 0.8582 (tm-30)
REVERT: C  198 ASP cc_start: 0.8415 (p0) cc_final: 0.8124 (p0)
REVERT: C  202 GLU cc_start: 0.8306 (mp0) cc_final: 0.8015 (mp0)
REVERT: D   26 MET cc_start: 0.9080 (mmp) cc_final: 0.8770 (mpp)
REVERT: D   59 TRP cc_start: 0.9258 (t60) cc_final: 0.8916 (t60)
REVERT: D  111 ASN cc_start: 0.9125 (t0) cc_final: 0.8784 (t0)
REVERT: D  197 ASP cc_start: 0.8861 (m-30) cc_final: 0.8660 (m-30)
REVERT: D  224 ASN cc_start: 0.9053 (m-40) cc_final: 0.8836 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1049
  time to fit residues: 39.6844
Evaluate side-chains
  201 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  87 HIS
B 184 HIS
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.099601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.072849 restraints weight = 22227.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.075014 restraints weight = 14212.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.076542 restraints weight = 10693.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.077464 restraints weight = 8830.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.077765 restraints weight = 7824.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   9017  Z= 0.310
  Angle     :  0.809  16.567  12160  Z= 0.407
  Chirality :  0.046   0.202   1334
  Planarity :  0.005   0.050   1548
  Dihedral  :  6.936  96.388   1229
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.29 %
    Favored  : 95.61 %
  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: -0.42 (0.25), residues: 1077
  helix:  0.63 (0.21), residues: 617
  sheet: -1.17 (0.58), residues: 58
  loop : -1.54 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 671 
 TYR   0.028   0.003   TYR C 128 
 PHE   0.030   0.003   PHE A 707 
 TRP   0.015   0.002   TRP A 476 
 HIS   0.010   0.002   HIS A 568 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00676 /  0.31 ( 9010)
  covalent geometry    : angle       0.79281 /  0.41 (12157)
  hydrogen bonds       : bond        0.04912 /  3.14 (  478)
  hydrogen bonds       : angle       4.95401 /  3.43 ( 1398)
  metal coordination   : bond        0.02520 /  1.51 (    7)
  metal coordination   : angle      10.15953 /  5.88 (    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
  224 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.446 
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  485 LEU cc_start: 0.9196 (mt) cc_final: 0.8941 (mt)
REVERT: A  501 GLU cc_start: 0.8405 (tp30) cc_final: 0.7925 (tp30)
REVERT: A  505 LEU cc_start: 0.9422 (mt) cc_final: 0.8712 (mt)
REVERT: A  544 ILE cc_start: 0.8745 (pt) cc_final: 0.7736 (tt)
REVERT: A  565 ASP cc_start: 0.8801 (t0) cc_final: 0.8485 (t0)
REVERT: A  698 LYS cc_start: 0.9233 (mmtp) cc_final: 0.8791 (mmmm)
REVERT: A  703 GLU cc_start: 0.8561 (tt0) cc_final: 0.8361 (tt0)
REVERT: A  723 LYS cc_start: 0.7651 (ptmt) cc_final: 0.7447 (pttt)
REVERT: B  146 MET cc_start: 0.9127 (mmm) cc_final: 0.8394 (mmm)
REVERT: B  195 ASN cc_start: 0.8652 (m-40) cc_final: 0.8354 (m110)
REVERT: B  197 LEU cc_start: 0.8358 (mm) cc_final: 0.7994 (mt)
REVERT: B  233 GLU cc_start: 0.7273 (pp20) cc_final: 0.6567 (pp20)
REVERT: B  242 VAL cc_start: 0.8784 (m) cc_final: 0.7092 (m)
REVERT: B  249 MET cc_start: 0.9257 (tmm) cc_final: 0.9006 (tmm)
REVERT: B  255 GLU cc_start: 0.8240 (tt0) cc_final: 0.8010 (tt0)
REVERT: B  319 ASN cc_start: 0.9290 (t0) cc_final: 0.8841 (t0)
REVERT: B  337 PHE cc_start: 0.9242 (t80) cc_final: 0.8961 (t80)
REVERT: B  341 CYS cc_start: 0.8567 (m) cc_final: 0.8277 (m)
REVERT: B  342 LEU cc_start: 0.8625 (mt) cc_final: 0.8321 (mt)
REVERT: B  374 TRP cc_start: 0.8630 (t60) cc_final: 0.8305 (t60)
REVERT: C  100 LEU cc_start: 0.8489 (mt) cc_final: 0.8274 (mt)
REVERT: C  149 TYR cc_start: 0.8401 (m-10) cc_final: 0.8179 (m-10)
REVERT: C  194 GLN cc_start: 0.8957 (tt0) cc_final: 0.8468 (tm-30)
REVERT: C  196 PHE cc_start: 0.8693 (t80) cc_final: 0.8435 (t80)
REVERT: C  198 ASP cc_start: 0.8194 (p0) cc_final: 0.7732 (p0)
REVERT: C  202 GLU cc_start: 0.8543 (mp0) cc_final: 0.8175 (mp0)
REVERT: C  207 ASN cc_start: 0.9019 (p0) cc_final: 0.8743 (p0)
REVERT: C  218 MET cc_start: 0.9278 (mmm) cc_final: 0.8782 (mmm)
REVERT: C  224 ASN cc_start: 0.9540 (m-40) cc_final: 0.9314 (m-40)
REVERT: D   26 MET cc_start: 0.9205 (mmp) cc_final: 0.8854 (mpp)
REVERT: D  111 ASN cc_start: 0.9073 (t0) cc_final: 0.8804 (t0)
REVERT: D  224 ASN cc_start: 0.9068 (m-40) cc_final: 0.8867 (m110)
  outliers start: 1
  outliers final: 1
  residues processed: 223
  average time/residue: 0.0859
  time to fit residues: 27.8091
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 62 optimal weight:   30.0000
   overall best weight:    1.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 512 ASN
** B  87 HIS ** 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 = 0.3580 r_free = 0.3580 target = 0.103527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.076556 restraints weight = 22687.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.079100 restraints weight = 14047.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.080797 restraints weight = 10268.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081817 restraints weight = 8331.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.082613 restraints weight = 7320.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9017  Z= 0.140
  Angle     :  0.639  11.674  12160  Z= 0.317
  Chirality :  0.042   0.174   1334
  Planarity :  0.004   0.036   1548
  Dihedral  :  6.566 100.976   1229
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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:  0.11 (0.26), residues: 1077
  helix:  1.12 (0.21), residues: 614
  sheet: -0.91 (0.56), residues: 68
  loop : -1.40 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 506 
 TYR   0.026   0.002   TYR A 656 
 PHE   0.036   0.002   PHE C 174 
 TRP   0.016   0.001   TRP B 247 
 HIS   0.003   0.001   HIS A 269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 ( 9010)
  covalent geometry    : angle       0.62925 /  0.32 (12157)
  hydrogen bonds       : bond        0.04008 /  2.57 (  478)
  hydrogen bonds       : angle       4.31742 /  2.99 ( 1398)
  metal coordination   : bond        0.01880 /  1.03 (    7)
  metal coordination   : angle       7.00319 /  4.08 (    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
  238 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.356 
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: 0.8347 (tp30) cc_final: 0.7727 (tp30)
REVERT: A  544 ILE cc_start: 0.8764 (pt) cc_final: 0.8442 (tt)
REVERT: A  547 LYS cc_start: 0.7338 (mmtt) cc_final: 0.7125 (mmtt)
REVERT: A  565 ASP cc_start: 0.8621 (t0) cc_final: 0.8338 (t0)
REVERT: A  591 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8012 (mttp)
REVERT: A  608 HIS cc_start: 0.6199 (p90) cc_final: 0.5808 (m170)
REVERT: A  640 TYR cc_start: 0.9280 (t80) cc_final: 0.8740 (t80)
REVERT: A  698 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8679 (mmmm)
REVERT: A  703 GLU cc_start: 0.8575 (tt0) cc_final: 0.8319 (tt0)
REVERT: A  723 LYS cc_start: 0.7676 (ptmt) cc_final: 0.7411 (pttt)
REVERT: B   94 MET cc_start: 0.4735 (pmm) cc_final: 0.4274 (pmm)
REVERT: B  146 MET cc_start: 0.8966 (mmm) cc_final: 0.8300 (mmm)
REVERT: B  180 LEU cc_start: 0.9163 (tp) cc_final: 0.8585 (tp)
REVERT: B  181 ARG cc_start: 0.8471 (mmp-170) cc_final: 0.8226 (mmm160)
REVERT: B  195 ASN cc_start: 0.8449 (m-40) cc_final: 0.8120 (m-40)
REVERT: B  197 LEU cc_start: 0.8218 (mm) cc_final: 0.7968 (mm)
REVERT: B  209 PHE cc_start: 0.9273 (p90) cc_final: 0.8966 (p90)
REVERT: B  230 MET cc_start: 0.7798 (tpp) cc_final: 0.7542 (tpp)
REVERT: B  233 GLU cc_start: 0.7012 (pp20) cc_final: 0.6255 (pp20)
REVERT: B  249 MET cc_start: 0.9176 (tmm) cc_final: 0.8933 (tmm)
REVERT: B  256 MET cc_start: 0.8872 (mtm) cc_final: 0.8610 (mtm)
REVERT: B  319 ASN cc_start: 0.9246 (t0) cc_final: 0.8775 (t0)
REVERT: B  341 CYS cc_start: 0.8575 (m) cc_final: 0.8305 (m)
REVERT: B  342 LEU cc_start: 0.8639 (mt) cc_final: 0.8266 (mt)
REVERT: B  374 TRP cc_start: 0.8512 (t60) cc_final: 0.8237 (t60)
REVERT: C   17 GLU cc_start: 0.7584 (mp0) cc_final: 0.7071 (mp0)
REVERT: C   74 ARG cc_start: 0.8039 (ptt180) cc_final: 0.7424 (ptt180)
REVERT: C  100 LEU cc_start: 0.8526 (mt) cc_final: 0.8299 (mt)
REVERT: C  194 GLN cc_start: 0.8976 (tt0) cc_final: 0.8492 (tm-30)
REVERT: C  198 ASP cc_start: 0.8183 (p0) cc_final: 0.7777 (p0)
REVERT: C  202 GLU cc_start: 0.8333 (mp0) cc_final: 0.8005 (mp0)
REVERT: C  207 ASN cc_start: 0.9099 (p0) cc_final: 0.8839 (p0)
REVERT: C  218 MET cc_start: 0.9281 (mmm) cc_final: 0.8886 (mmm)
REVERT: C  224 ASN cc_start: 0.9537 (m-40) cc_final: 0.7926 (m-40)
REVERT: C  228 TRP cc_start: 0.8939 (m-10) cc_final: 0.8332 (m-90)
REVERT: D   59 TRP cc_start: 0.9291 (t60) cc_final: 0.8899 (t60)
REVERT: D  111 ASN cc_start: 0.9092 (t0) cc_final: 0.8842 (t0)
REVERT: D  224 ASN cc_start: 0.9050 (m-40) cc_final: 0.8816 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0869
  time to fit residues: 29.5711
Evaluate side-chains
  181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3512 r_free = 0.3512 target = 0.099417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.073394 restraints weight = 21626.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.075552 restraints weight = 13987.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.077039 restraints weight = 10538.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.078014 restraints weight = 8703.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.078390 restraints weight = 7692.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.5475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9017  Z= 0.240
  Angle     :  0.711  12.760  12160  Z= 0.354
  Chirality :  0.043   0.201   1334
  Planarity :  0.004   0.039   1548
  Dihedral  :  6.627 103.443   1229
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  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 (0.26), residues: 1077
  helix:  1.15 (0.21), residues: 615
  sheet: -0.68 (0.59), residues: 58
  loop : -1.39 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 506 
 TYR   0.026   0.002   TYR C 178 
 PHE   0.018   0.002   PHE A 707 
 TRP   0.017   0.002   TRP B 247 
 HIS   0.013   0.002   HIS B 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00528 /  0.24 ( 9010)
  covalent geometry    : angle       0.69866 /  0.35 (12157)
  hydrogen bonds       : bond        0.04173 /  2.70 (  478)
  hydrogen bonds       : angle       4.54543 /  3.14 ( 1398)
  metal coordination   : bond        0.02224 /  1.23 (    7)
  metal coordination   : angle       8.42823 /  4.79 (    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
  207 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.381 
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  501 GLU cc_start: 0.8353 (tp30) cc_final: 0.7951 (tp30)
REVERT: A  505 LEU cc_start: 0.9324 (mt) cc_final: 0.8724 (mt)
REVERT: A  544 ILE cc_start: 0.8822 (pt) cc_final: 0.7858 (tt)
REVERT: A  565 ASP cc_start: 0.8620 (t0) cc_final: 0.8251 (t0)
REVERT: A  591 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8041 (mttp)
REVERT: A  698 LYS cc_start: 0.9131 (mmtp) cc_final: 0.8578 (mmmm)
REVERT: A  703 GLU cc_start: 0.8638 (tt0) cc_final: 0.8404 (tt0)
REVERT: B   94 MET cc_start: 0.4890 (pmm) cc_final: 0.4388 (pmm)
REVERT: B  146 MET cc_start: 0.9019 (mmm) cc_final: 0.8339 (mmm)
REVERT: B  180 LEU cc_start: 0.9110 (tp) cc_final: 0.8199 (tp)
REVERT: B  181 ARG cc_start: 0.8574 (mmp-170) cc_final: 0.8354 (mmm160)
REVERT: B  209 PHE cc_start: 0.9277 (p90) cc_final: 0.8772 (p90)
REVERT: B  233 GLU cc_start: 0.7223 (pp20) cc_final: 0.6441 (pp20)
REVERT: B  249 MET cc_start: 0.9194 (tmm) cc_final: 0.8963 (tmm)
REVERT: B  308 MET cc_start: 0.7243 (ttp) cc_final: 0.6558 (tmm)
REVERT: B  319 ASN cc_start: 0.9234 (t0) cc_final: 0.8702 (t0)
REVERT: B  337 PHE cc_start: 0.9249 (t80) cc_final: 0.9007 (t80)
REVERT: B  341 CYS cc_start: 0.8521 (m) cc_final: 0.8316 (m)
REVERT: B  374 TRP cc_start: 0.8547 (t60) cc_final: 0.8329 (t60)
REVERT: C   17 GLU cc_start: 0.7637 (mp0) cc_final: 0.7088 (mp0)
REVERT: C  202 GLU cc_start: 0.8449 (mp0) cc_final: 0.8135 (mp0)
REVERT: C  207 ASN cc_start: 0.9091 (p0) cc_final: 0.8745 (p0)
REVERT: D   26 MET cc_start: 0.9217 (mmp) cc_final: 0.8737 (mpp)
REVERT: D   59 TRP cc_start: 0.9326 (t60) cc_final: 0.8942 (t60)
REVERT: D  111 ASN cc_start: 0.9060 (t0) cc_final: 0.8819 (t0)
REVERT: D  224 ASN cc_start: 0.9007 (m-40) cc_final: 0.8785 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0795
  time to fit residues: 23.9513
Evaluate side-chains
  163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 45 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3549 r_free = 0.3549 target = 0.101401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.076089 restraints weight = 16401.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.077968 restraints weight = 11267.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.079086 restraints weight = 8846.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.079951 restraints weight = 7624.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.080253 restraints weight = 6860.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9017  Z= 0.170
  Angle     :  0.668  11.705  12160  Z= 0.333
  Chirality :  0.042   0.172   1334
  Planarity :  0.004   0.034   1548
  Dihedral  :  6.681 105.862   1229
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  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:  0.32 (0.26), residues: 1077
  helix:  1.33 (0.21), residues: 610
  sheet: -1.10 (0.62), residues: 57
  loop : -1.31 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 506 
 TYR   0.017   0.002   TYR D 178 
 PHE   0.045   0.002   PHE C 174 
 TRP   0.018   0.001   TRP B 247 
 HIS   0.013   0.002   HIS D 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 9010)
  covalent geometry    : angle       0.65989 /  0.33 (12157)
  hydrogen bonds       : bond        0.04029 /  2.59 (  478)
  hydrogen bonds       : angle       4.39181 /  3.04 ( 1398)
  metal coordination   : bond        0.02169 /  1.17 (    7)
  metal coordination   : angle       6.54312 /  3.62 (    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
  214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.349 
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  501 GLU cc_start: 0.8338 (tp30) cc_final: 0.8048 (tp30)
REVERT: A  505 LEU cc_start: 0.9387 (mt) cc_final: 0.8792 (mt)
REVERT: A  544 ILE cc_start: 0.8735 (pt) cc_final: 0.8391 (tt)
REVERT: A  564 MET cc_start: 0.8230 (tpp) cc_final: 0.7849 (tpp)
REVERT: A  565 ASP cc_start: 0.8578 (t0) cc_final: 0.8256 (t0)
REVERT: A  591 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8106 (mttp)
REVERT: A  640 TYR cc_start: 0.9257 (t80) cc_final: 0.8561 (t80)
REVERT: A  698 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8485 (mmmm)
REVERT: A  703 GLU cc_start: 0.8703 (tt0) cc_final: 0.8460 (tt0)
REVERT: B   94 MET cc_start: 0.4587 (pmm) cc_final: 0.4136 (pmm)
REVERT: B  146 MET cc_start: 0.9052 (mmm) cc_final: 0.8323 (mmm)
REVERT: B  155 LEU cc_start: 0.9703 (tt) cc_final: 0.9449 (mm)
REVERT: B  180 LEU cc_start: 0.9201 (tp) cc_final: 0.8357 (tp)
REVERT: B  209 PHE cc_start: 0.8995 (p90) cc_final: 0.8470 (p90)
REVERT: B  233 GLU cc_start: 0.7237 (pp20) cc_final: 0.6464 (pp20)
REVERT: B  249 MET cc_start: 0.9168 (tmm) cc_final: 0.8946 (tmm)
REVERT: B  319 ASN cc_start: 0.9218 (t0) cc_final: 0.8665 (t0)
REVERT: B  337 PHE cc_start: 0.9229 (t80) cc_final: 0.8977 (t80)
REVERT: B  341 CYS cc_start: 0.8433 (m) cc_final: 0.8146 (m)
REVERT: B  374 TRP cc_start: 0.8580 (t60) cc_final: 0.8361 (t60)
REVERT: C   17 GLU cc_start: 0.7648 (mp0) cc_final: 0.7060 (mp0)
REVERT: C  111 ASN cc_start: 0.8507 (t0) cc_final: 0.8153 (t0)
REVERT: C  150 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8333 (mm-40)
REVERT: C  179 TYR cc_start: 0.9126 (t80) cc_final: 0.8822 (t80)
REVERT: C  203 LEU cc_start: 0.9177 (mt) cc_final: 0.8794 (mp)
REVERT: C  207 ASN cc_start: 0.9137 (p0) cc_final: 0.8759 (p0)
REVERT: C  224 ASN cc_start: 0.9383 (m-40) cc_final: 0.7407 (m-40)
REVERT: C  228 TRP cc_start: 0.8994 (m-10) cc_final: 0.8202 (m-90)
REVERT: D   59 TRP cc_start: 0.9297 (t60) cc_final: 0.8884 (t60)
REVERT: D  111 ASN cc_start: 0.9116 (t0) cc_final: 0.8841 (t0)
REVERT: D  224 ASN cc_start: 0.9001 (m-40) cc_final: 0.8773 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0807
  time to fit residues: 25.2153
Evaluate side-chains
  170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 45 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0370
   chunk 82 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 661 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.103390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.077351 restraints weight = 21477.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.079790 restraints weight = 13063.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.081452 restraints weight = 9590.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.082426 restraints weight = 7820.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.082974 restraints weight = 6857.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9017  Z= 0.122
  Angle     :  0.619  10.748  12160  Z= 0.310
  Chirality :  0.041   0.174   1334
  Planarity :  0.004   0.040   1548
  Dihedral  :  6.461 108.024   1229
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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:  1.59 (0.21), residues: 609
  sheet: -1.09 (0.56), residues: 67
  loop : -1.25 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 181 
 TYR   0.017   0.002   TYR D 125 
 PHE   0.057   0.002   PHE C 174 
 TRP   0.016   0.001   TRP B 247 
 HIS   0.008   0.001   HIS D 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 9010)
  covalent geometry    : angle       0.61599 /  0.31 (12157)
  hydrogen bonds       : bond        0.03780 /  2.45 (  478)
  hydrogen bonds       : angle       4.08811 /  2.82 ( 1398)
  metal coordination   : bond        0.00672 /  0.34 (    7)
  metal coordination   : angle       4.23398 /  2.33 (    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
  227 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LEU cc_start: 0.8076 (tp) cc_final: 0.7838 (tp)
REVERT: A  501 GLU cc_start: 0.8330 (tp30) cc_final: 0.8032 (tp30)
REVERT: A  505 LEU cc_start: 0.9325 (mt) cc_final: 0.8718 (mt)
REVERT: A  544 ILE cc_start: 0.8715 (pt) cc_final: 0.7761 (tt)
REVERT: A  673 TYR cc_start: 0.8827 (m-10) cc_final: 0.8606 (m-10)
REVERT: A  698 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8504 (mmmm)
REVERT: A  703 GLU cc_start: 0.8693 (tt0) cc_final: 0.8417 (tt0)
REVERT: B   94 MET cc_start: 0.3923 (pmm) cc_final: 0.3516 (pmm)
REVERT: B  108 ARG cc_start: 0.9281 (ptt180) cc_final: 0.8993 (ptp90)
REVERT: B  146 MET cc_start: 0.8997 (mmm) cc_final: 0.8234 (mmm)
REVERT: B  155 LEU cc_start: 0.9691 (tt) cc_final: 0.9439 (mm)
REVERT: B  180 LEU cc_start: 0.9147 (tp) cc_final: 0.8329 (tp)
REVERT: B  195 ASN cc_start: 0.8399 (m110) cc_final: 0.8150 (m-40)
REVERT: B  209 PHE cc_start: 0.8931 (p90) cc_final: 0.8321 (p90)
REVERT: B  233 GLU cc_start: 0.7155 (pp20) cc_final: 0.6360 (pp20)
REVERT: B  249 MET cc_start: 0.9142 (tmm) cc_final: 0.8927 (tmm)
REVERT: B  319 ASN cc_start: 0.9073 (t0) cc_final: 0.8478 (t0)
REVERT: B  337 PHE cc_start: 0.9246 (t80) cc_final: 0.9010 (t80)
REVERT: B  341 CYS cc_start: 0.8386 (m) cc_final: 0.8083 (m)
REVERT: C   17 GLU cc_start: 0.7535 (mp0) cc_final: 0.7078 (mp0)
REVERT: C  111 ASN cc_start: 0.8536 (t0) cc_final: 0.8140 (t0)
REVERT: C  194 GLN cc_start: 0.8934 (tt0) cc_final: 0.8377 (tm-30)
REVERT: C  198 ASP cc_start: 0.7890 (p0) cc_final: 0.7519 (p0)
REVERT: C  203 LEU cc_start: 0.9015 (mt) cc_final: 0.8709 (mp)
REVERT: C  207 ASN cc_start: 0.9126 (p0) cc_final: 0.8755 (p0)
REVERT: C  218 MET cc_start: 0.8641 (tpp) cc_final: 0.8201 (mmm)
REVERT: C  224 ASN cc_start: 0.9364 (m-40) cc_final: 0.7553 (m-40)
REVERT: C  228 TRP cc_start: 0.8891 (m-10) cc_final: 0.8236 (m-90)
REVERT: D   26 MET cc_start: 0.9269 (mmt) cc_final: 0.8800 (mpp)
REVERT: D   59 TRP cc_start: 0.9270 (t60) cc_final: 0.8855 (t60)
REVERT: D  111 ASN cc_start: 0.9005 (t0) cc_final: 0.8709 (t0)
REVERT: D  224 ASN cc_start: 0.8940 (m-40) cc_final: 0.8704 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0788
  time to fit residues: 25.9064
Evaluate side-chains
  176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 62 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 82 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 HIS
D 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.075204 restraints weight = 21674.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.077519 restraints weight = 13511.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.078941 restraints weight = 10041.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.079992 restraints weight = 8330.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.080717 restraints weight = 7347.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.6066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9017  Z= 0.160
  Angle     :  0.664  10.690  12160  Z= 0.329
  Chirality :  0.042   0.278   1334
  Planarity :  0.004   0.046   1548
  Dihedral  :  6.488 109.861   1229
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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:  1.57 (0.21), residues: 611
  sheet: -0.85 (0.58), residues: 61
  loop : -1.26 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 189 
 TYR   0.020   0.002   TYR A 566 
 PHE   0.027   0.002   PHE B 129 
 TRP   0.032   0.002   TRP B 374 
 HIS   0.010   0.001   HIS D 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 9010)
  covalent geometry    : angle       0.65977 /  0.33 (12157)
  hydrogen bonds       : bond        0.03857 /  2.49 (  478)
  hydrogen bonds       : angle       4.20606 /  2.90 ( 1398)
  metal coordination   : bond        0.01489 /  0.81 (    7)
  metal coordination   : angle       4.85872 /  2.77 (    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
  214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 GLU cc_start: 0.8368 (tp30) cc_final: 0.8094 (tp30)
REVERT: A  505 LEU cc_start: 0.9396 (mt) cc_final: 0.8895 (mt)
REVERT: A  544 ILE cc_start: 0.8666 (pt) cc_final: 0.8325 (tt)
REVERT: A  640 TYR cc_start: 0.8991 (t80) cc_final: 0.8737 (t80)
REVERT: A  698 LYS cc_start: 0.9164 (mmtp) cc_final: 0.8600 (mmmm)
REVERT: A  703 GLU cc_start: 0.8739 (tt0) cc_final: 0.8467 (tt0)
REVERT: B   94 MET cc_start: 0.4059 (pmm) cc_final: 0.3672 (pmm)
REVERT: B  108 ARG cc_start: 0.9278 (ptt180) cc_final: 0.9018 (ptp90)
REVERT: B  146 MET cc_start: 0.9060 (mmm) cc_final: 0.8340 (mmm)
REVERT: B  155 LEU cc_start: 0.9701 (tt) cc_final: 0.9441 (mm)
REVERT: B  180 LEU cc_start: 0.9184 (tp) cc_final: 0.8411 (tp)
REVERT: B  195 ASN cc_start: 0.8533 (m110) cc_final: 0.8276 (m-40)
REVERT: B  209 PHE cc_start: 0.8750 (p90) cc_final: 0.8412 (p90)
REVERT: B  233 GLU cc_start: 0.7191 (pp20) cc_final: 0.6368 (pp20)
REVERT: B  247 TRP cc_start: 0.9286 (t-100) cc_final: 0.9025 (t-100)
REVERT: B  249 MET cc_start: 0.9209 (tmm) cc_final: 0.8937 (tmm)
REVERT: B  319 ASN cc_start: 0.9049 (t0) cc_final: 0.8451 (t0)
REVERT: B  341 CYS cc_start: 0.8409 (m) cc_final: 0.8176 (m)
REVERT: C   17 GLU cc_start: 0.7546 (mp0) cc_final: 0.7072 (mp0)
REVERT: C  111 ASN cc_start: 0.8550 (t0) cc_final: 0.8140 (t0)
REVERT: C  207 ASN cc_start: 0.9126 (p0) cc_final: 0.8704 (p0)
REVERT: C  218 MET cc_start: 0.8749 (tpp) cc_final: 0.8188 (mmm)
REVERT: C  224 ASN cc_start: 0.9384 (m-40) cc_final: 0.7504 (m-40)
REVERT: C  228 TRP cc_start: 0.8909 (m-10) cc_final: 0.8374 (m-90)
REVERT: D   26 MET cc_start: 0.9320 (mmt) cc_final: 0.8832 (mpp)
REVERT: D  111 ASN cc_start: 0.9038 (t0) cc_final: 0.8723 (t0)
REVERT: D  224 ASN cc_start: 0.8966 (m-40) cc_final: 0.8693 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0836
  time to fit residues: 25.8438
Evaluate side-chains
  164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   chunk 103 optimal weight:    0.3980
   chunk 43 optimal weight:    8.9990
   chunk 37 optimal weight:    0.1980
   chunk 4 optimal weight:    9.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  87 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 = 0.3590 r_free = 0.3590 target = 0.103508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.077794 restraints weight = 21182.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.080364 restraints weight = 12892.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.081990 restraints weight = 9345.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.083081 restraints weight = 7588.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.083573 restraints weight = 6617.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.6123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9017  Z= 0.120
  Angle     :  0.631  11.621  12160  Z= 0.315
  Chirality :  0.041   0.172   1334
  Planarity :  0.004   0.043   1548
  Dihedral  :  6.354 110.725   1229
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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:  0.71 (0.26), residues: 1077
  helix:  1.61 (0.21), residues: 611
  sheet: -0.71 (0.58), residues: 72
  loop : -1.12 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 260 
 TYR   0.030   0.002   TYR D 178 
 PHE   0.052   0.002   PHE C 174 
 TRP   0.026   0.001   TRP B 374 
 HIS   0.009   0.001   HIS B 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 9010)
  covalent geometry    : angle       0.62576 /  0.31 (12157)
  hydrogen bonds       : bond        0.03690 /  2.38 (  478)
  hydrogen bonds       : angle       4.11292 /  2.84 ( 1398)
  metal coordination   : bond        0.00705 /  0.41 (    7)
  metal coordination   : angle       5.44028 /  3.13 (    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
  220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.347 
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  255 LEU cc_start: 0.8067 (tp) cc_final: 0.7841 (tp)
REVERT: A  501 GLU cc_start: 0.8283 (tp30) cc_final: 0.8030 (tp30)
REVERT: A  505 LEU cc_start: 0.9361 (mt) cc_final: 0.8828 (mt)
REVERT: A  544 ILE cc_start: 0.8638 (pt) cc_final: 0.8316 (tt)
REVERT: A  640 TYR cc_start: 0.8883 (t80) cc_final: 0.8682 (t80)
REVERT: A  698 LYS cc_start: 0.9062 (mmtp) cc_final: 0.8598 (mmmm)
REVERT: A  703 GLU cc_start: 0.8734 (tt0) cc_final: 0.8437 (tt0)
REVERT: B   94 MET cc_start: 0.4005 (pmm) cc_final: 0.3625 (pmm)
REVERT: B  108 ARG cc_start: 0.9249 (ptt180) cc_final: 0.8944 (ptp90)
REVERT: B  146 MET cc_start: 0.8998 (mmm) cc_final: 0.8276 (mmm)
REVERT: B  155 LEU cc_start: 0.9695 (tt) cc_final: 0.9422 (mm)
REVERT: B  180 LEU cc_start: 0.9162 (tp) cc_final: 0.8332 (tp)
REVERT: B  209 PHE cc_start: 0.8681 (p90) cc_final: 0.8402 (p90)
REVERT: B  233 GLU cc_start: 0.7193 (pp20) cc_final: 0.6410 (pp20)
REVERT: B  249 MET cc_start: 0.9146 (tmm) cc_final: 0.8885 (tmm)
REVERT: B  319 ASN cc_start: 0.8977 (t0) cc_final: 0.8546 (p0)
REVERT: B  341 CYS cc_start: 0.8378 (m) cc_final: 0.8122 (m)
REVERT: C   17 GLU cc_start: 0.7576 (mp0) cc_final: 0.7174 (mp0)
REVERT: C  111 ASN cc_start: 0.8524 (t0) cc_final: 0.8130 (t0)
REVERT: C  207 ASN cc_start: 0.9200 (p0) cc_final: 0.8743 (p0)
REVERT: C  218 MET cc_start: 0.8697 (tpp) cc_final: 0.8154 (mmm)
REVERT: C  224 ASN cc_start: 0.9386 (m-40) cc_final: 0.7520 (m-40)
REVERT: C  228 TRP cc_start: 0.8873 (m-10) cc_final: 0.8363 (m-90)
REVERT: D   26 MET cc_start: 0.9313 (mmt) cc_final: 0.8864 (mpp)
REVERT: D  111 ASN cc_start: 0.8992 (t0) cc_final: 0.8679 (t0)
REVERT: D  224 ASN cc_start: 0.8930 (m-40) cc_final: 0.8653 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0813
  time to fit residues: 26.0425
Evaluate side-chains
  170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0570
   chunk 65 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0980
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.0100

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  87 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 = 0.3581 r_free = 0.3581 target = 0.103091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.077881 restraints weight = 21325.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080244 restraints weight = 13303.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.081848 restraints weight = 9795.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.082453 restraints weight = 7966.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.083313 restraints weight = 7167.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.6241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9017  Z= 0.129
  Angle     :  0.654  14.137  12160  Z= 0.321
  Chirality :  0.041   0.172   1334
  Planarity :  0.004   0.042   1548
  Dihedral  :  6.348 112.588   1229
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  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:  1.66 (0.21), residues: 611
  sheet: -0.77 (0.58), residues: 61
  loop : -1.14 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  74 
 TYR   0.023   0.002   TYR A 673 
 PHE   0.029   0.002   PHE A 707 
 TRP   0.025   0.002   TRP B 374 
 HIS   0.008   0.001   HIS D 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 9010)
  covalent geometry    : angle       0.64799 /  0.32 (12157)
  hydrogen bonds       : bond        0.03676 /  2.37 (  478)
  hydrogen bonds       : angle       4.09947 /  2.84 ( 1398)
  metal coordination   : bond        0.00938 /  0.50 (    7)
  metal coordination   : angle       5.64907 /  3.26 (    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
  210 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LEU cc_start: 0.8081 (tp) cc_final: 0.7865 (tp)
REVERT: A  501 GLU cc_start: 0.8317 (tp30) cc_final: 0.8078 (tp30)
REVERT: A  505 LEU cc_start: 0.9380 (mt) cc_final: 0.8852 (mt)
REVERT: A  544 ILE cc_start: 0.8660 (pt) cc_final: 0.8315 (tt)
REVERT: A  640 TYR cc_start: 0.8949 (t80) cc_final: 0.8688 (t80)
REVERT: A  698 LYS cc_start: 0.9073 (mmtp) cc_final: 0.8609 (mmmm)
REVERT: A  703 GLU cc_start: 0.8742 (tt0) cc_final: 0.8508 (tt0)
REVERT: B   94 MET cc_start: 0.4033 (pmm) cc_final: 0.3640 (pmm)
REVERT: B  108 ARG cc_start: 0.9249 (ptt180) cc_final: 0.8929 (ptp90)
REVERT: B  146 MET cc_start: 0.8977 (mmm) cc_final: 0.8300 (mmm)
REVERT: B  155 LEU cc_start: 0.9691 (tt) cc_final: 0.9417 (mm)
REVERT: B  180 LEU cc_start: 0.9173 (tp) cc_final: 0.8328 (tp)
REVERT: B  195 ASN cc_start: 0.8518 (m110) cc_final: 0.8023 (t0)
REVERT: B  209 PHE cc_start: 0.8676 (p90) cc_final: 0.8388 (p90)
REVERT: B  233 GLU cc_start: 0.7193 (pp20) cc_final: 0.6386 (pp20)
REVERT: B  249 MET cc_start: 0.9169 (tmm) cc_final: 0.8896 (tmm)
REVERT: B  319 ASN cc_start: 0.8946 (t0) cc_final: 0.8532 (p0)
REVERT: C   17 GLU cc_start: 0.7568 (mp0) cc_final: 0.7176 (mp0)
REVERT: C  111 ASN cc_start: 0.8518 (t0) cc_final: 0.8136 (t0)
REVERT: C  207 ASN cc_start: 0.9203 (p0) cc_final: 0.8781 (p0)
REVERT: C  218 MET cc_start: 0.8679 (tpp) cc_final: 0.8162 (mmm)
REVERT: C  224 ASN cc_start: 0.9369 (m-40) cc_final: 0.7288 (m-40)
REVERT: C  228 TRP cc_start: 0.8864 (m-10) cc_final: 0.8300 (m-90)
REVERT: D   26 MET cc_start: 0.9293 (mmt) cc_final: 0.8813 (mpp)
REVERT: D   59 TRP cc_start: 0.9240 (t60) cc_final: 0.8890 (t60)
REVERT: D  111 ASN cc_start: 0.9003 (t0) cc_final: 0.8734 (t0)
REVERT: D  224 ASN cc_start: 0.8891 (m-40) cc_final: 0.8624 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0854
  time to fit residues: 25.8566
Evaluate side-chains
  166 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 106 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 73 optimal weight:    0.0570
   chunk 92 optimal weight:   10.0000
   chunk 7 optimal weight:    0.4980
   chunk 38 optimal weight:   20.0000
   chunk 43 optimal weight:    7.9990
   overall best weight:    1.4702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 335 GLN
D 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.102475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.076198 restraints weight = 21466.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.078555 restraints weight = 13379.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.080106 restraints weight = 9861.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.081139 restraints weight = 8116.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.081514 restraints weight = 7132.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9017  Z= 0.142
  Angle     :  0.643  10.944  12160  Z= 0.321
  Chirality :  0.042   0.170   1334
  Planarity :  0.004   0.042   1548
  Dihedral  :  6.300 113.481   1229
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  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:  0.82 (0.26), residues: 1077
  helix:  1.75 (0.21), residues: 611
  sheet: -0.72 (0.60), residues: 59
  loop : -1.15 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 260 
 TYR   0.020   0.002   TYR D 178 
 PHE   0.018   0.001   PHE A 268 
 TRP   0.025   0.002   TRP B 247 
 HIS   0.008   0.001   HIS D 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 9010)
  covalent geometry    : angle       0.63742 /  0.32 (12157)
  hydrogen bonds       : bond        0.03684 /  2.38 (  478)
  hydrogen bonds       : angle       4.08667 /  2.83 ( 1398)
  metal coordination   : bond        0.01196 /  0.67 (    7)
  metal coordination   : angle       5.64689 /  3.24 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1604.26 seconds
wall clock time: 28 minutes 29.27 seconds (1709.27 seconds total)