Starting phenix.real_space_refine
on Wed Nov 19 00:02:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ifz_9659/11_2025/6ifz_9659.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ifz_9659/11_2025/6ifz_9659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ifz_9659/11_2025/6ifz_9659.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ifz_9659/11_2025/6ifz_9659.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ifz_9659/11_2025/6ifz_9659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ifz_9659/11_2025/6ifz_9659.map"
  }
  resolution = 3.58
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      62      5.49       5
     S      37      5.16       5
     C   12029      2.51       5
     N    3257      2.21       5
     O    3799      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19185
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 5799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 734, 5799
          Classifications: {'peptide': 734}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 8, 'TRANS': 725}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 144
          Unresolved non-hydrogen angles: 178
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 7, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "D"
      Number of atoms: 995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 995
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 985
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1695
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "F"
      Number of atoms: 1697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1697
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 209}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1623
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 201}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2319
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 281}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "H"
      Number of atoms: 2750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2750
          Classifications: {'peptide': 345}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 17, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "I"
      Number of atoms: 715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 715
          Classifications: {'RNA': 34}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 16, 'rna3p': 17}
    Chain: "J"
      Number of atoms: 606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 606
          Classifications: {'RNA': 28}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 3, 'rna3p': 24}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2935  SG  CYS A 404      55.785  30.462  65.300  1.00 51.21           S
  ATOM   3079  SG  CYS A 422      58.862  33.242  65.609  1.00 46.39           S

  Time building chain proxies: 5.08, per 1000 atoms: 0.26
  Number of scatterers: 19185
  At special positions: 0
  Unit cell: (93.6, 135.2, 174.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     P      62     15.00
     O    3799      8.00
     N    3257      7.00
     C   12029      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 818.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 404 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 422 "


  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4254

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 23 sheets defined
      37.2% alpha, 11.2% beta
      21 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 2.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 15
    Processing helix  chain 'A' and resid 17 through 25
      removed outlier: 3.805A  pdb=" N   ILE A  21 " --> pdb=" O   ILE A  17 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   ARG A  23 " --> pdb=" O   LYS A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 40
      removed outlier: 3.832A  pdb=" N   ALA A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASP A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 4.341A  pdb=" N   GLN A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 3.639A  pdb=" N   THR A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 3.856A  pdb=" N   TYR A 141 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLU A 142 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 138 through 142'
    Processing helix  chain 'A' and resid 145 through 148
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 4.048A  pdb=" N   ARG A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 3.821A  pdb=" N   ASN A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 4.041A  pdb=" N   PHE A 183 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL A 184 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 184'
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 4.958A  pdb=" N   ARG A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS A 219 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.682A  pdb=" N   PHE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 266 through 291
      removed outlier: 3.964A  pdb=" N   ARG A 272 " --> pdb=" O   GLN A 268 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ALA A 284 " --> pdb=" O   SER A 280 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   LEU A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP A 289 " --> pdb=" O   ASP A 285 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 335
      removed outlier: 3.690A  pdb=" N   THR A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN A 334 " --> pdb=" O   PHE A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 378
      removed outlier: 4.213A  pdb=" N   TYR A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   GLN A 365 " --> pdb=" O   GLU A 361 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA A 370 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 3.824A  pdb=" N   ASN A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 432
      removed outlier: 4.608A  pdb=" N   TYR A 426 " --> pdb=" O   CYS A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 462
      removed outlier: 4.022A  pdb=" N   SER A 462 " --> pdb=" O   GLU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 503
      removed outlier: 3.684A  pdb=" N   LYS A 503 " --> pdb=" O   ALA A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 529
      removed outlier: 3.776A  pdb=" N   ALA A 529 " --> pdb=" O   ALA A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 558
    Processing helix  chain 'A' and resid 559 through 564
    Processing helix  chain 'A' and resid 584 through 603
      removed outlier: 4.219A  pdb=" N   LYS A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 638
      removed outlier: 3.586A  pdb=" N   GLN A 628 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 659
      removed outlier: 3.609A  pdb=" N   ILE A 659 " --> pdb=" O   PHE A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 675
    Processing helix  chain 'A' and resid 681 through 695
      removed outlier: 3.978A  pdb=" N   ILE A 685 " --> pdb=" O   GLY A 681 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   HIS A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 712
      removed outlier: 3.773A  pdb=" N   ALA A 701 " --> pdb=" O   ARG A 697 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLU A 712 " --> pdb=" O   THR A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 732
      removed outlier: 3.795A  pdb=" N   LEU A 728 " --> pdb=" O   THR A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 755
    Processing helix  chain 'D' and resid 8 through 18
      removed outlier: 3.652A  pdb=" N   ALA D  16 " --> pdb=" O   ILE D  12 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ILE D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 57
      removed outlier: 3.569A  pdb=" N   LEU D  40 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU D  46 " --> pdb=" O   ASN D  42 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR D  47 " --> pdb=" O   LEU D  43 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   THR D  49 " --> pdb=" O   SER D  45 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   LEU D  50 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 78
      removed outlier: 4.029A  pdb=" N   VAL D  71 " --> pdb=" O   ALA D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 90
      removed outlier: 4.111A  pdb=" N   GLU D  88 " --> pdb=" O   LYS D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 97
      removed outlier: 3.626A  pdb=" N   LYS D  97 " --> pdb=" O   LEU D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 122
      removed outlier: 4.166A  pdb=" N   ARG D 107 " --> pdb=" O   GLU D 103 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR D 122 " --> pdb=" O   TYR D 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 18
    Processing helix  chain 'C' and resid 37 through 55
      removed outlier: 4.749A  pdb=" N   LEU C  43 " --> pdb=" O   LYS C  39 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   LEU C  46 " --> pdb=" O   ASN C  42 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   THR C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU C  53 " --> pdb=" O   THR C  49 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LYS C  55 " --> pdb=" O   PHE C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 62
    Processing helix  chain 'C' and resid 64 through 78
      removed outlier: 3.765A  pdb=" N   ARG C  70 " --> pdb=" O   ILE C  66 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL C  74 " --> pdb=" O   ARG C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 101 through 122
    Processing helix  chain 'G' and resid 48 through 62
      removed outlier: 3.542A  pdb=" N   LEU G  52 " --> pdb=" O   PRO G  48 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS G  55 " --> pdb=" O   SER G  51 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   THR G  58 " --> pdb=" O   GLY G  54 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 162 through 177
      removed outlier: 3.742A  pdb=" N   ASP G 166 " --> pdb=" O   GLN G 162 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE G 167 " --> pdb=" O   VAL G 163 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   LYS G 168 " --> pdb=" O   GLU G 164 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL G 169 " --> pdb=" O   GLU G 165 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP G 172 " --> pdb=" O   LYS G 168 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 61
      removed outlier: 3.669A  pdb=" N   LEU F  52 " --> pdb=" O   PRO F  48 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   MET F  56 " --> pdb=" O   LEU F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 76 through 83
      removed outlier: 3.527A  pdb=" N   SER F  80 " --> pdb=" O   SER F  76 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG F  81 " --> pdb=" O   ASP F  77 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU F  82 " --> pdb=" O   ILE F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 107 through 112
    Processing helix  chain 'F' and resid 162 through 180
      removed outlier: 3.634A  pdb=" N   PHE F 167 " --> pdb=" O   VAL F 163 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS F 168 " --> pdb=" O   GLU F 164 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL F 169 " --> pdb=" O   GLU F 165 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP F 172 " --> pdb=" O   LYS F 168 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 185 through 189
      removed outlier: 3.523A  pdb=" N   GLY F 189 " --> pdb=" O   GLY F 186 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 211
      removed outlier: 3.550A  pdb=" N   THR F 211 " --> pdb=" O   ASP F 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 208 through 211'
    Processing helix  chain 'F' and resid 212 through 217
      removed outlier: 3.867A  pdb=" N   LEU F 216 " --> pdb=" O   LEU F 212 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 61
      removed outlier: 3.873A  pdb=" N   LYS E  55 " --> pdb=" O   SER E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 83
    Processing helix  chain 'E' and resid 107 through 113
    Processing helix  chain 'E' and resid 162 through 165
    Processing helix  chain 'E' and resid 166 through 178
      removed outlier: 4.171A  pdb=" N   ASP E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU E 176 " --> pdb=" O   ASP E 172 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU E 178 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 185 through 189
      removed outlier: 3.804A  pdb=" N   GLY E 189 " --> pdb=" O   GLY E 186 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 212 through 217
    Processing helix  chain 'B' and resid 29 through 40
    Processing helix  chain 'B' and resid 45 through 54
    Processing helix  chain 'B' and resid 96 through 101
    Processing helix  chain 'B' and resid 110 through 118
      removed outlier: 4.024A  pdb=" N   LEU B 115 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN B 116 " --> pdb=" O   ASP B 112 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLU B 118 " --> pdb=" O   TYR B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 181 through 185
      removed outlier: 3.540A  pdb=" N   GLY B 185 " --> pdb=" O   ARG B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.649A  pdb=" N   ASP B 202 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'H' and resid 42 through 51
    Processing helix  chain 'H' and resid 52 through 54
      No H-bonds generated for 'chain 'H' and resid 52 through 54'
    Processing helix  chain 'H' and resid 55 through 64
      removed outlier: 3.582A  pdb=" N   LEU H  63 " --> pdb=" O   PHE H  59 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ILE H  64 " --> pdb=" O   GLU H  60 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 69 through 73
    Processing helix  chain 'H' and resid 75 through 80
    Processing helix  chain 'H' and resid 128 through 144
      removed outlier: 3.591A  pdb=" N   LEU H 132 " --> pdb=" O   PRO H 128 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   THR H 138 " --> pdb=" O   GLY H 134 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE H 139 " --> pdb=" O   ALA H 135 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR H 144 " --> pdb=" O   LEU H 140 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 145 through 148
      removed outlier: 4.065A  pdb=" N   ASN H 148 " --> pdb=" O   PRO H 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 145 through 148'
    Processing helix  chain 'H' and resid 236 through 245
      removed outlier: 3.663A  pdb=" N   LEU H 242 " --> pdb=" O   GLU H 238 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 245 through 259
      removed outlier: 4.558A  pdb=" N   GLN H 251 " --> pdb=" O   GLY H 247 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 266 through 270
    Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108
      removed outlier: 4.418A  pdb=" N   GLN A 107 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301
    Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 301
    Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 448
      removed outlier: 6.517A  pdb=" N   ALA A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   HIS A 436 " --> pdb=" O   VAL A 456 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 569 through 574
      removed outlier: 4.754A  pdb=" N   ILE A 571 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ILE A 582 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY A 612 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 96 through 97
    Processing sheet with id=AA7, first strand: chain 'G' and resid 102 through 103
      removed outlier: 4.161A  pdb=" N   PHE G 102 " --> pdb=" O   ASP G 148 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LYS G   5 " --> pdb=" O   VAL G 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 118 through 122
    Processing sheet with id=AA9, first strand: chain 'F' and resid 146 through 149
    Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 149
      removed outlier: 7.037A  pdb=" N   LYS F   5 " --> pdb=" O   THR F 202 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   THR F 202 " --> pdb=" O   LYS F   5 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LYS F   7 " --> pdb=" O   ALA F 200 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ALA F 200 " --> pdb=" O   LYS F   7 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   SER F   9 " --> pdb=" O   LEU F 198 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LEU F 198 " --> pdb=" O   SER F   9 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 123
    Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149
      removed outlier: 6.301A  pdb=" N   SER E   9 " --> pdb=" O   LEU E 198 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU E 198 " --> pdb=" O   SER E   9 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 39
      removed outlier: 3.748A  pdb=" N   LEU E  44 " --> pdb=" O   ASP E  39 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 123
    Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.020A  pdb=" N   PHE B  64 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL B 158 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ALA B 160 " --> pdb=" O   LYS B   4 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   LYS B   4 " --> pdb=" O   ALA B 160 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AB9, first strand: chain 'B' and resid 127 through 128
    Processing sheet with id=AC1, first strand: chain 'B' and resid 131 through 134
      removed outlier: 3.512A  pdb=" N   TYR B 143 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 211 through 213
    Processing sheet with id=AC3, first strand: chain 'H' and resid 227 through 230
    Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 33
    Processing sheet with id=AC5, first strand: chain 'H' and resid 203 through 206

    598 hydrogen bonds defined for protein.
    1677 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      100 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 3.35

  Time building geometry restraints manager: 2.37 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 3478
        1.32 -     1.45: 5330
        1.45 -     1.57: 10677
        1.57 -     1.69: 123
        1.69 -     1.82: 66
  Bond restraints: 19674
  Sorted by residual:
  bond pdb=" C   GLN H 275 "
       pdb=" N   TYR H 276 "
    ideal  model  delta    sigma   weight residual
    1.331  1.422 -0.091 2.07e-02 2.33e+03 1.95e+01
  bond pdb=" N   TYR G 181 "
       pdb=" CA  TYR G 181 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.32e-02 5.74e+03 9.20e+00
  bond pdb=" N   LEU A 160 "
       pdb=" CA  LEU A 160 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.16e-02 7.43e+03 8.07e+00
  bond pdb=" CA  ARG H 158 "
       pdb=" C   ARG H 158 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.040 1.41e-02 5.03e+03 7.89e+00
  bond pdb=" N   ILE E  29 "
       pdb=" CA  ILE E  29 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.47e+00
  ... (remaining 19669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 26440
        3.77 -     7.54: 342
        7.54 -    11.32: 37
       11.32 -    15.09: 8
       15.09 -    18.86: 2
  Bond angle restraints: 26829
  Sorted by residual:
  angle pdb=" N   GLY H 314 "
        pdb=" CA  GLY H 314 "
        pdb=" C   GLY H 314 "
      ideal   model   delta    sigma   weight residual
     112.73  127.67  -14.94 1.20e+00 6.94e-01 1.55e+02
  angle pdb=" N   SER H 107 "
        pdb=" CA  SER H 107 "
        pdb=" C   SER H 107 "
      ideal   model   delta    sigma   weight residual
     112.45   95.21   17.24 1.39e+00 5.18e-01 1.54e+02
  angle pdb=" N   ARG F  95 "
        pdb=" CA  ARG F  95 "
        pdb=" C   ARG F  95 "
      ideal   model   delta    sigma   weight residual
     112.24  126.42  -14.18 1.28e+00 6.10e-01 1.23e+02
  angle pdb=" N   ARG E  95 "
        pdb=" CA  ARG E  95 "
        pdb=" C   ARG E  95 "
      ideal   model   delta    sigma   weight residual
     112.24  125.39  -13.15 1.28e+00 6.10e-01 1.06e+02
  angle pdb=" N   LYS H 161 "
        pdb=" CA  LYS H 161 "
        pdb=" C   LYS H 161 "
      ideal   model   delta    sigma   weight residual
     110.23  121.06  -10.83 1.45e+00 4.76e-01 5.57e+01
  ... (remaining 26824 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.04: 11448
       34.04 -    68.07: 398
       68.07 -   102.11: 33
      102.11 -   136.15: 1
      136.15 -   170.19: 3
  Dihedral angle restraints: 11883
    sinusoidal: 5288
      harmonic: 6595
  Sorted by residual:
  dihedral pdb=" CA  TYR B  78 "
           pdb=" C   TYR B  78 "
           pdb=" N   PRO B  79 "
           pdb=" CA  PRO B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   45.13  134.87     0      5.00e+00 4.00e-02 7.28e+02
  dihedral pdb=" O4'   C I  14 "
           pdb=" C1'   C I  14 "
           pdb=" N1    C I  14 "
           pdb=" C2    C I  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   42.19 -170.19     1      1.70e+01 3.46e-03 6.59e+01
  dihedral pdb=" O4'   C I   8 "
           pdb=" C1'   C I   8 "
           pdb=" N1    C I   8 "
           pdb=" C2    C I   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   34.41 -162.41     1      1.70e+01 3.46e-03 6.49e+01
  ... (remaining 11880 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 2849
       0.119 -    0.239: 159
       0.239 -    0.358: 14
       0.358 -    0.477: 4
       0.477 -    0.596: 3
  Chirality restraints: 3029
  Sorted by residual:
  chirality pdb=" CA  PHE H 159 "
            pdb=" N   PHE H 159 "
            pdb=" C   PHE H 159 "
            pdb=" CB  PHE H 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.89e+00
  chirality pdb=" CA  ARG F  95 "
            pdb=" N   ARG F  95 "
            pdb=" C   ARG F  95 "
            pdb=" CB  ARG F  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.71e+00
  chirality pdb=" CA  ARG E  95 "
            pdb=" N   ARG E  95 "
            pdb=" C   ARG E  95 "
            pdb=" CB  ARG E  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.40e+00
  ... (remaining 3026 not shown)

  Planarity restraints: 3226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G I  21 "    0.066 2.00e-02 2.50e+03   2.89e-02 2.50e+01
        pdb=" N9    G I  21 "   -0.071 2.00e-02 2.50e+03
        pdb=" C8    G I  21 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G I  21 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G I  21 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G I  21 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G I  21 "    0.024 2.00e-02 2.50e+03
        pdb=" N1    G I  21 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G I  21 "    0.000 2.00e-02 2.50e+03
        pdb=" N2    G I  21 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    G I  21 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    G I  21 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 638 "    0.023 2.00e-02 2.50e+03   4.74e-02 2.25e+01
        pdb=" C   GLY A 638 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   GLY A 638 "    0.031 2.00e-02 2.50e+03
        pdb=" N   ASN A 639 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A I  27 "    0.055 2.00e-02 2.50e+03   2.62e-02 1.88e+01
        pdb=" N9    A I  27 "   -0.065 2.00e-02 2.50e+03
        pdb=" C8    A I  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A I  27 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A I  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A I  27 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A I  27 "    0.015 2.00e-02 2.50e+03
        pdb=" N1    A I  27 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A I  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A I  27 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4    A I  27 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 3223 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 7
        1.99 -     2.71: 1307
        2.71 -     3.44: 26631
        3.44 -     4.17: 47514
        4.17 -     4.90: 85260
  Nonbonded interactions: 160719
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 639 "
            pdb=" OG  SER A 643 "
     model   vdw
     1.258 3.120
  nonbonded pdb=" CD1 LEU H 225 "
            pdb=" CD2 LEU H 335 "
     model   vdw
     1.771 3.880
  nonbonded pdb=" CD2 LEU C  46 "
            pdb=" O   ALA G  25 "
     model   vdw
     1.838 3.460
  nonbonded pdb=" OG1 THR H  97 "
            pdb=" O   ILE H 198 "
     model   vdw
     1.873 3.040
  nonbonded pdb=" CG  MET B   8 "
            pdb=" O   LEU B 156 "
     model   vdw
     1.930 3.440
  ... (remaining 160714 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'
  selection = (chain 'D' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 26 through 99 or (resid 100 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 101 through 123))
}
ncs_group {
  reference = (chain 'E' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 161 through 217))
  selection = (chain 'F' and (resid 2 through 66 or resid 76 through 156 or (resid 157 through \ 
 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throu \ 
gh 217))
  selection = (chain 'G' and (resid 2 through 66 or resid 76 through 158 or (resid 159 through \ 
 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throu \ 
gh 217))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     23.170
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
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      :  0.009   0.294  19677  Z= 0.406
  Angle     :  1.149  18.860  26829  Z= 0.656
  Chirality :  0.067   0.596   3029
  Planarity :  0.006   0.060   3226
  Dihedral  : 17.374 170.186   7629
  Min Nonbonded Distance : 1.258

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 10.74 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.93 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -5.16 (0.13), residues: 2226
  helix: -3.36 (0.12), residues: 785
  sheet: -3.36 (0.23), residues: 362
  loop : -3.46 (0.14), residues: 1079

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG G 136 
 TYR   0.028   0.003   TYR D   9 
 PHE   0.045   0.003   PHE F  98 
 TRP   0.066   0.003   TRP A 732 
 HIS   0.008   0.002   HIS A 695 

Details of bonding type rmsd
  covalent geometry    : bond        0.00837 (19674)
  covalent geometry    : angle       1.14895 (26829)
  hydrogen bonds       : bond        0.17704 (  630)
  hydrogen bonds       : angle       7.97612 ( 1777)
  metal coordination   : bond        0.26834 (    2)
  Misc. bond           : bond        0.06567 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  541 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 523
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 ILE cc_start: 0.7013 (tp) cc_final: 0.6494 (tt)
REVERT: A  183 PHE cc_start: 0.6605 (m-80) cc_final: 0.6281 (m-80)
REVERT: A  228 LEU cc_start: 0.7736 (mp) cc_final: 0.7318 (tp)
REVERT: A  384 TYR cc_start: 0.6242 (t80) cc_final: 0.6015 (t80)
REVERT: A  527 PHE cc_start: 0.6481 (t80) cc_final: 0.5536 (m-10)
REVERT: A  623 SER cc_start: 0.8495 (m) cc_final: 0.8269 (p)
REVERT: A  641 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6452 (tttp)
REVERT: D   22 ARG cc_start: 0.6446 (mpt-90) cc_final: 0.6178 (mpt-90)
REVERT: D   44 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8691 (tp)
REVERT: G    8 PHE cc_start: 0.7715 (m-80) cc_final: 0.7475 (m-80)
REVERT: G   70 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6229 (tp30)
REVERT: G  127 ASP cc_start: 0.7909 (t0) cc_final: 0.7683 (t0)
REVERT: E  156 THR cc_start: 0.6417 (t) cc_final: 0.5931 (p)
REVERT: B  219 LEU cc_start: 0.8059 (tt) cc_final: 0.7686 (tp)
REVERT: B  278 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7891 (ttm170)
REVERT: H   50 MET cc_start: 0.7759 (tmm) cc_final: 0.7552 (tmm)
REVERT: H  158 ARG cc_start: 0.7564 (mpt180) cc_final: 0.6325 (ttp-170)
REVERT: H  319 THR cc_start: 0.9284 (p) cc_final: 0.8499 (p)
REVERT: H  345 MET cc_start: 0.8329 (tpt) cc_final: 0.7715 (tpt)
  outliers start: 18
  outliers final: 8
  residues processed: 539
  average time/residue: 0.1612
  time to fit residues: 127.2847
Evaluate side-chains
  306 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 296
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  639 ASN
Chi-restraints excluded: chain A residue  641 LYS
Chi-restraints excluded: chain D residue   44 LEU
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain E residue   24 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain H residue  167 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 216 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 200 optimal weight:    0.9990
   chunk 212 optimal weight:    0.9980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
A 175 ASN
A 436 HIS
A 497 ASN
A 676 HIS
A 695 HIS
A 699 ASN
A 727 ASN
D  72 GLN
G  11 GLN
G  85 ASN
G 159 ASN
F  33 ASN
F 213 ASN
E 144 ASN
B  11 GLN
B  81 HIS
B 135 GLN
B 137 HIS
B 144 GLN
B 152 ASN
B 174 GLN
B 284 HIS
H  22 ASN
H 148 ASN
H 194 ASN
H 275 GLN

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.140975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121211 restraints weight = 31891.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.122963 restraints weight = 26123.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124424 restraints weight = 19081.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.124343 restraints weight = 14103.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.124542 restraints weight = 13418.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  19677  Z= 0.148
  Angle     :  0.698  11.931  26829  Z= 0.368
  Chirality :  0.045   0.386   3029
  Planarity :  0.004   0.080   3226
  Dihedral  : 15.140 168.329   3404
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.40 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.41 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -3.97 (0.15), residues: 2226
  helix: -1.91 (0.16), residues: 764
  sheet: -3.06 (0.24), residues: 346
  loop : -3.03 (0.16), residues: 1116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  22 
 TYR   0.017   0.002   TYR A  74 
 PHE   0.022   0.002   PHE C  51 
 TRP   0.036   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (19674)
  covalent geometry    : angle       0.69787 (26829)
  hydrogen bonds       : bond        0.03786 (  630)
  hydrogen bonds       : angle       5.31644 ( 1777)
  metal coordination   : bond        0.00188 (    2)
  Misc. bond           : bond        0.00024 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  436 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 385
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: A  183 PHE cc_start: 0.6506 (m-80) cc_final: 0.6170 (m-80)
REVERT: A  278 PHE cc_start: 0.7826 (m-10) cc_final: 0.7618 (m-10)
REVERT: A  384 TYR cc_start: 0.6257 (t80) cc_final: 0.5927 (t80)
REVERT: A  388 MET cc_start: 0.7334 (ttm) cc_final: 0.7109 (ttm)
REVERT: A  426 TYR cc_start: 0.7200 (t80) cc_final: 0.6894 (t80)
REVERT: A  527 PHE cc_start: 0.6691 (t80) cc_final: 0.5426 (m-10)
REVERT: A  622 ILE cc_start: 0.8699 (mp) cc_final: 0.8431 (mt)
REVERT: A  728 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8160 (tp)
REVERT: D    7 GLU cc_start: 0.7418 (pm20) cc_final: 0.7192 (pm20)
REVERT: D   44 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8497 (tp)
REVERT: G   64 TYR cc_start: 0.7503 (m-10) cc_final: 0.6973 (m-10)
REVERT: G  124 ASN cc_start: 0.8633 (p0) cc_final: 0.8208 (p0)
REVERT: G  171 ARG cc_start: 0.6661 (tmm-80) cc_final: 0.6414 (mmm160)
REVERT: E   46 ILE cc_start: 0.8673 (tt) cc_final: 0.8387 (mm)
REVERT: E  129 ILE cc_start: 0.7921 (mm) cc_final: 0.7704 (mm)
REVERT: E  146 THR cc_start: 0.8070 (p) cc_final: 0.7790 (p)
REVERT: E  174 LEU cc_start: 0.8819 (mt) cc_final: 0.8533 (mp)
REVERT: B  219 LEU cc_start: 0.8045 (tt) cc_final: 0.7697 (mt)
REVERT: B  278 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7801 (ttm170)
REVERT: H  158 ARG cc_start: 0.7354 (mpt180) cc_final: 0.6375 (ttt90)
REVERT: H  164 LYS cc_start: 0.7580 (mttt) cc_final: 0.7237 (tppt)
REVERT: H  221 SER cc_start: 0.7692 (p) cc_final: 0.7416 (m)
  outliers start: 51
  outliers final: 23
  residues processed: 417
  average time/residue: 0.1506
  time to fit residues: 94.9039
Evaluate side-chains
  317 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 292
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   21 GLU
Chi-restraints excluded: chain D residue   44 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue  119 GLU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain H residue  167 ILE
Chi-restraints excluded: chain H residue  199 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 197 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 166 optimal weight:    0.9980
   chunk 191 optimal weight:    3.9990
   chunk 159 optimal weight:    6.9990
   chunk 162 optimal weight:    0.9990
   chunk 124 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 190 optimal weight:    4.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
A 268 GLN
A 312 ASN
A 497 ASN
C  42 ASN
E 144 ASN
B 152 ASN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 275 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.138328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.118224 restraints weight = 32458.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.120163 restraints weight = 27503.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.120765 restraints weight = 20864.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.120985 restraints weight = 16298.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.121333 restraints weight = 15098.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  19677  Z= 0.196
  Angle     :  0.693  13.020  26829  Z= 0.362
  Chirality :  0.045   0.395   3029
  Planarity :  0.004   0.063   3226
  Dihedral  : 14.842 172.831   3393
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.57 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.28 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -3.54 (0.16), residues: 2226
  helix: -1.41 (0.17), residues: 781
  sheet: -2.85 (0.24), residues: 352
  loop : -2.89 (0.16), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 128 
 TYR   0.033   0.002   TYR A  74 
 PHE   0.018   0.002   PHE G 167 
 TRP   0.028   0.002   TRP A 732 
 HIS   0.005   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (19674)
  covalent geometry    : angle       0.69347 (26829)
  hydrogen bonds       : bond        0.03717 (  630)
  hydrogen bonds       : angle       5.04810 ( 1777)
  metal coordination   : bond        0.00211 (    2)
  Misc. bond           : bond        0.00001 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 319
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 PHE cc_start: 0.6532 (m-80) cc_final: 0.6155 (m-80)
REVERT: A  278 PHE cc_start: 0.7866 (m-10) cc_final: 0.7611 (m-10)
REVERT: A  527 PHE cc_start: 0.5812 (t80) cc_final: 0.5365 (m-80)
REVERT: A  633 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7695 (tm-30)
REVERT: A  728 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8283 (tp)
REVERT: D    4 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (pp)
REVERT: D    7 GLU cc_start: 0.7573 (pm20) cc_final: 0.7278 (pm20)
REVERT: D   44 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8455 (tp)
REVERT: C   46 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8842 (mt)
REVERT: G   64 TYR cc_start: 0.7560 (m-10) cc_final: 0.7067 (m-10)
REVERT: G  124 ASN cc_start: 0.8731 (p0) cc_final: 0.8411 (p0)
REVERT: F   79 LEU cc_start: 0.7708 (mp) cc_final: 0.7467 (tt)
REVERT: F  172 ASP cc_start: 0.6904 (m-30) cc_final: 0.6656 (m-30)
REVERT: B  219 LEU cc_start: 0.8181 (tt) cc_final: 0.7916 (mt)
REVERT: H  158 ARG cc_start: 0.7517 (mpt180) cc_final: 0.6609 (ttp-170)
REVERT: H  164 LYS cc_start: 0.7709 (mttt) cc_final: 0.7359 (tppt)
  outliers start: 66
  outliers final: 41
  residues processed: 361
  average time/residue: 0.1553
  time to fit residues: 85.3511
Evaluate side-chains
  326 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 280
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  633 GLU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   44 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain C residue   11 ASP
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue  120 VAL
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue  134 ASN
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain H residue   94 ILE
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  167 ILE
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  274 LEU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 160 optimal weight:    4.9990
   chunk 159 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 226 optimal weight:    6.9990
   chunk 177 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 137 GLN
F 162 GLN
B 152 ASN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.121800 restraints weight = 31924.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.123766 restraints weight = 26468.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125034 restraints weight = 18446.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.125216 restraints weight = 13979.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125511 restraints weight = 14474.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  19677  Z= 0.125
  Angle     :  0.619  11.064  26829  Z= 0.324
  Chirality :  0.043   0.363   3029
  Planarity :  0.004   0.061   3226
  Dihedral  : 14.656 172.413   3393
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.00 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.87 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -3.16 (0.16), residues: 2226
  helix: -0.98 (0.18), residues: 791
  sheet: -2.66 (0.26), residues: 338
  loop : -2.78 (0.16), residues: 1097

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  81 
 TYR   0.026   0.001   TYR A  74 
 PHE   0.033   0.001   PHE B  64 
 TRP   0.027   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (19674)
  covalent geometry    : angle       0.61934 (26829)
  hydrogen bonds       : bond        0.03217 (  630)
  hydrogen bonds       : angle       4.67427 ( 1777)
  metal coordination   : bond        0.00149 (    2)
  Misc. bond           : bond        0.00033 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 342
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A  183 PHE cc_start: 0.6607 (m-80) cc_final: 0.6118 (m-80)
REVERT: A  351 LYS cc_start: 0.7350 (mmpt) cc_final: 0.6461 (tptt)
REVERT: A  527 PHE cc_start: 0.5843 (t80) cc_final: 0.5329 (m-80)
REVERT: A  622 ILE cc_start: 0.8677 (mp) cc_final: 0.8421 (mt)
REVERT: A  728 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8231 (tp)
REVERT: D    7 GLU cc_start: 0.7444 (pm20) cc_final: 0.7225 (pm20)
REVERT: C   69 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9228 (mp)
REVERT: G   64 TYR cc_start: 0.7428 (m-10) cc_final: 0.6895 (m-10)
REVERT: G  124 ASN cc_start: 0.8499 (p0) cc_final: 0.8108 (p0)
REVERT: F   89 LYS cc_start: 0.7673 (tppp) cc_final: 0.7437 (mtpt)
REVERT: F  123 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7501 (mt-10)
REVERT: B    5 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8049 (pp)
REVERT: B  219 LEU cc_start: 0.8074 (tt) cc_final: 0.7828 (mt)
REVERT: H   43 MET cc_start: 0.7986 (mmm) cc_final: 0.7350 (mmm)
REVERT: H  158 ARG cc_start: 0.7237 (mpt180) cc_final: 0.6484 (ttt-90)
REVERT: H  164 LYS cc_start: 0.7463 (mttt) cc_final: 0.7151 (tppt)
  outliers start: 69
  outliers final: 40
  residues processed: 385
  average time/residue: 0.1580
  time to fit residues: 91.8738
Evaluate side-chains
  341 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 297
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   21 GLU
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue  119 GLU
Chi-restraints excluded: chain F residue  123 GLU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  167 ILE
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  274 LEU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 144 optimal weight:    5.9990
   chunk 45 optimal weight:   20.0000
   chunk 201 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 100 optimal weight:    0.2980
   chunk 203 optimal weight:   40.0000
   chunk 220 optimal weight:    9.9990
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 ASN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.139344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.119028 restraints weight = 32194.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.120157 restraints weight = 28193.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.121842 restraints weight = 22784.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121656 restraints weight = 17653.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.122544 restraints weight = 17890.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  19677  Z= 0.183
  Angle     :  0.657  11.617  26829  Z= 0.343
  Chirality :  0.045   0.380   3029
  Planarity :  0.004   0.058   3226
  Dihedral  : 14.605 172.138   3390
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.94 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 20.57 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -3.03 (0.16), residues: 2226
  helix: -0.85 (0.18), residues: 798
  sheet: -2.54 (0.25), residues: 346
  loop : -2.75 (0.17), residues: 1082

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 188 
 TYR   0.022   0.002   TYR A  74 
 PHE   0.023   0.002   PHE B  64 
 TRP   0.021   0.002   TRP A 732 
 HIS   0.005   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (19674)
  covalent geometry    : angle       0.65675 (26829)
  hydrogen bonds       : bond        0.03443 (  630)
  hydrogen bonds       : angle       4.70605 ( 1777)
  metal coordination   : bond        0.00265 (    2)
  Misc. bond           : bond        0.00005 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 316
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 PHE cc_start: 0.6646 (m-80) cc_final: 0.6104 (m-80)
REVERT: A  351 LYS cc_start: 0.7327 (mmpt) cc_final: 0.6510 (tptt)
REVERT: A  527 PHE cc_start: 0.5837 (t80) cc_final: 0.5344 (m-80)
REVERT: A  622 ILE cc_start: 0.8659 (mp) cc_final: 0.8409 (mt)
REVERT: A  728 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8075 (tp)
REVERT: D    7 GLU cc_start: 0.7381 (pm20) cc_final: 0.7127 (pm20)
REVERT: D   75 TYR cc_start: 0.8922 (t80) cc_final: 0.8684 (t80)
REVERT: D   85 ASP cc_start: 0.7379 (t0) cc_final: 0.7142 (t0)
REVERT: C   15 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8126 (mtmm)
REVERT: G   64 TYR cc_start: 0.7398 (m-10) cc_final: 0.6827 (m-10)
REVERT: G  124 ASN cc_start: 0.8685 (p0) cc_final: 0.8369 (p0)
REVERT: G  164 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7128 (pm20)
REVERT: G  168 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6604 (tppt)
REVERT: F   79 LEU cc_start: 0.7660 (mp) cc_final: 0.7403 (tt)
REVERT: F   89 LYS cc_start: 0.7774 (tppp) cc_final: 0.7515 (mtpt)
REVERT: E  171 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6856 (mtp-110)
REVERT: B  219 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7872 (mt)
REVERT: H  158 ARG cc_start: 0.7372 (mpt180) cc_final: 0.6552 (ttt-90)
REVERT: H  164 LYS cc_start: 0.7570 (mttt) cc_final: 0.7264 (tppt)
  outliers start: 79
  outliers final: 52
  residues processed: 376
  average time/residue: 0.1610
  time to fit residues: 91.2841
Evaluate side-chains
  352 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 296
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue   19 HIS
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   70 GLU
Chi-restraints excluded: chain G residue  132 GLU
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   80 SER
Chi-restraints excluded: chain F residue  134 ASN
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  171 ARG
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  167 ILE
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  229 GLU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 70 optimal weight:    0.2980
   chunk 10 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
D  72 GLN
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 ASN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.117742 restraints weight = 32113.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118191 restraints weight = 27213.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.120129 restraints weight = 23639.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.120024 restraints weight = 16804.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.120380 restraints weight = 17333.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  19677  Z= 0.207
  Angle     :  0.684  12.278  26829  Z= 0.356
  Chirality :  0.045   0.391   3029
  Planarity :  0.004   0.060   3226
  Dihedral  : 14.638 171.581   3390
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.25 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 21.59 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -2.92 (0.17), residues: 2226
  helix: -0.76 (0.18), residues: 793
  sheet: -2.46 (0.26), residues: 345
  loop : -2.69 (0.17), residues: 1088

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 128 
 TYR   0.021   0.002   TYR A  74 
 PHE   0.031   0.002   PHE A 548 
 TRP   0.019   0.002   TRP A 732 
 HIS   0.005   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (19674)
  covalent geometry    : angle       0.68373 (26829)
  hydrogen bonds       : bond        0.03550 (  630)
  hydrogen bonds       : angle       4.78695 ( 1777)
  metal coordination   : bond        0.00341 (    2)
  Misc. bond           : bond        0.00010 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 304
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 PHE cc_start: 0.6645 (m-80) cc_final: 0.6047 (m-80)
REVERT: A  351 LYS cc_start: 0.7379 (mmpt) cc_final: 0.6541 (tptt)
REVERT: A  527 PHE cc_start: 0.5868 (t80) cc_final: 0.5365 (m-80)
REVERT: A  728 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8098 (tp)
REVERT: D    7 GLU cc_start: 0.7485 (pm20) cc_final: 0.7266 (pm20)
REVERT: D   96 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (tt)
REVERT: G   64 TYR cc_start: 0.7455 (m-10) cc_final: 0.6881 (m-10)
REVERT: G  124 ASN cc_start: 0.8763 (p0) cc_final: 0.8456 (p0)
REVERT: G  164 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6942 (pm20)
REVERT: G  168 LYS cc_start: 0.7007 (mmmt) cc_final: 0.6643 (tppt)
REVERT: F   89 LYS cc_start: 0.7789 (tppp) cc_final: 0.7512 (mtpt)
REVERT: E  171 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6700 (mtp-110)
REVERT: B   78 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6751 (t80)
REVERT: B  219 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7877 (mt)
REVERT: H  158 ARG cc_start: 0.7497 (mpt180) cc_final: 0.6551 (ttt-90)
REVERT: H  164 LYS cc_start: 0.7594 (mttt) cc_final: 0.7254 (tppt)
  outliers start: 87
  outliers final: 60
  residues processed: 365
  average time/residue: 0.1513
  time to fit residues: 85.0279
Evaluate side-chains
  354 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 288
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  384 TYR
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue   19 HIS
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   44 LEU
Chi-restraints excluded: chain G residue   70 GLU
Chi-restraints excluded: chain G residue  132 GLU
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   80 SER
Chi-restraints excluded: chain F residue  134 ASN
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  152 ILE
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  171 ARG
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  167 ILE
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  229 GLU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 127 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 201 optimal weight:    1.9990
   chunk 217 optimal weight:    0.6980
   chunk 212 optimal weight:    0.8980
   chunk 211 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
D  72 GLN
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 ASN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.140139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.119796 restraints weight = 32148.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.120779 restraints weight = 27633.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122193 restraints weight = 23062.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122177 restraints weight = 16630.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.122712 restraints weight = 16673.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  19677  Z= 0.155
  Angle     :  0.650  11.008  26829  Z= 0.336
  Chirality :  0.044   0.373   3029
  Planarity :  0.004   0.055   3226
  Dihedral  : 14.515 171.825   3390
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.67 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 22.66 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -2.74 (0.17), residues: 2226
  helix: -0.54 (0.18), residues: 785
  sheet: -2.34 (0.26), residues: 345
  loop : -2.63 (0.17), residues: 1096

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 136 
 TYR   0.019   0.001   TYR A  74 
 PHE   0.031   0.002   PHE A 548 
 TRP   0.021   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (19674)
  covalent geometry    : angle       0.65001 (26829)
  hydrogen bonds       : bond        0.03315 (  630)
  hydrogen bonds       : angle       4.65895 ( 1777)
  metal coordination   : bond        0.00197 (    2)
  Misc. bond           : bond        0.00005 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 321
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 PHE cc_start: 0.6668 (m-80) cc_final: 0.6036 (m-80)
REVERT: A  351 LYS cc_start: 0.7380 (mmpt) cc_final: 0.6505 (tptt)
REVERT: A  527 PHE cc_start: 0.5906 (t80) cc_final: 0.5433 (m-80)
REVERT: A  728 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8071 (tp)
REVERT: G   64 TYR cc_start: 0.7421 (m-10) cc_final: 0.6833 (m-10)
REVERT: G  124 ASN cc_start: 0.8655 (p0) cc_final: 0.8356 (p0)
REVERT: G  164 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7022 (pm20)
REVERT: G  168 LYS cc_start: 0.7011 (mmmt) cc_final: 0.6660 (tppt)
REVERT: E  171 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6618 (mtp-110)
REVERT: B   78 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6724 (t80)
REVERT: B  219 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7879 (mt)
REVERT: H  158 ARG cc_start: 0.7318 (mpt180) cc_final: 0.6441 (ttt-90)
REVERT: H  164 LYS cc_start: 0.7519 (mttt) cc_final: 0.7250 (tppt)
  outliers start: 82
  outliers final: 59
  residues processed: 376
  average time/residue: 0.1494
  time to fit residues: 86.6347
Evaluate side-chains
  355 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 291
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  384 TYR
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  570 SER
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue   19 HIS
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   44 LEU
Chi-restraints excluded: chain G residue   70 GLU
Chi-restraints excluded: chain G residue  132 GLU
Chi-restraints excluded: chain G residue  146 THR
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   80 SER
Chi-restraints excluded: chain F residue  119 GLU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  152 ILE
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  171 ARG
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  167 ILE
Chi-restraints excluded: chain H residue  173 LYS
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 180 optimal weight:    0.0970
   chunk 174 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 210 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9990
   chunk 136 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 226 optimal weight:    7.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D  72 GLN
G 137 GLN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.143612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.123649 restraints weight = 32010.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.126119 restraints weight = 26018.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126834 restraints weight = 18657.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.126945 restraints weight = 14158.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127276 restraints weight = 13482.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  19677  Z= 0.116
  Angle     :  0.625  10.379  26829  Z= 0.322
  Chirality :  0.043   0.349   3029
  Planarity :  0.003   0.057   3226
  Dihedral  : 14.365 172.454   3390
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.00 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.16 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -2.48 (0.17), residues: 2226
  helix: -0.32 (0.18), residues: 792
  sheet: -2.23 (0.26), residues: 341
  loop : -2.49 (0.17), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 136 
 TYR   0.028   0.001   TYR A 300 
 PHE   0.039   0.001   PHE B  64 
 TRP   0.022   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (19674)
  covalent geometry    : angle       0.62455 (26829)
  hydrogen bonds       : bond        0.03131 (  630)
  hydrogen bonds       : angle       4.53012 ( 1777)
  metal coordination   : bond        0.00093 (    2)
  Misc. bond           : bond        0.00016 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 337
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: A  351 LYS cc_start: 0.7310 (mmpt) cc_final: 0.6499 (tptt)
REVERT: A  728 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.7916 (tp)
REVERT: G  124 ASN cc_start: 0.8484 (p0) cc_final: 0.8132 (p0)
REVERT: G  164 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6975 (pm20)
REVERT: G  190 TYR cc_start: 0.8097 (m-80) cc_final: 0.7773 (m-80)
REVERT: F  105 ASN cc_start: 0.8736 (p0) cc_final: 0.8530 (p0)
REVERT: E  171 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6488 (mtp-110)
REVERT: B  219 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7864 (mt)
REVERT: H  254 TYR cc_start: 0.8430 (t80) cc_final: 0.8122 (t80)
  outliers start: 57
  outliers final: 43
  residues processed: 372
  average time/residue: 0.1523
  time to fit residues: 86.6690
Evaluate side-chains
  354 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 307
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  570 SER
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue   19 HIS
Chi-restraints excluded: chain G residue   70 GLU
Chi-restraints excluded: chain G residue  132 GLU
Chi-restraints excluded: chain G residue  146 THR
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   80 SER
Chi-restraints excluded: chain F residue  119 GLU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  171 ARG
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  173 LYS
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 225 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 187 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 145 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 174 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 124 optimal weight:    0.7980
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
D  72 GLN
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 137 GLN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.117326 restraints weight = 32282.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.117829 restraints weight = 27292.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.119297 restraints weight = 23450.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.119328 restraints weight = 17200.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.119485 restraints weight = 18018.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  19677  Z= 0.225
  Angle     :  0.711  14.056  26829  Z= 0.369
  Chirality :  0.046   0.383   3029
  Planarity :  0.004   0.053   3226
  Dihedral  : 14.487 171.638   3386
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.34 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 23.89 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -2.65 (0.17), residues: 2226
  helix: -0.48 (0.18), residues: 794
  sheet: -2.19 (0.26), residues: 351
  loop : -2.62 (0.17), residues: 1081

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 185 
 TYR   0.026   0.002   TYR E  64 
 PHE   0.041   0.002   PHE B  64 
 TRP   0.027   0.002   TRP A 732 
 HIS   0.005   0.001   HIS E  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (19674)
  covalent geometry    : angle       0.71124 (26829)
  hydrogen bonds       : bond        0.03762 (  630)
  hydrogen bonds       : angle       4.82802 ( 1777)
  metal coordination   : bond        0.00297 (    2)
  Misc. bond           : bond        0.00000 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 288
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A  351 LYS cc_start: 0.7373 (mmpt) cc_final: 0.6530 (tptt)
REVERT: A  728 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8049 (tp)
REVERT: D   85 ASP cc_start: 0.7567 (t0) cc_final: 0.7222 (t0)
REVERT: G   64 TYR cc_start: 0.7488 (m-10) cc_final: 0.6895 (m-10)
REVERT: G  124 ASN cc_start: 0.8696 (p0) cc_final: 0.8420 (p0)
REVERT: G  164 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7061 (pm20)
REVERT: E  171 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6519 (mtp-110)
REVERT: B   78 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.7023 (t80)
REVERT: B  219 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7890 (mt)
  outliers start: 64
  outliers final: 50
  residues processed: 331
  average time/residue: 0.1458
  time to fit residues: 75.1863
Evaluate side-chains
  333 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 278
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  570 SER
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue   19 HIS
Chi-restraints excluded: chain G residue  132 GLU
Chi-restraints excluded: chain G residue  146 THR
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   80 SER
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain E residue   50 SER
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  152 ILE
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  171 ARG
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   15 LEU
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  173 LYS
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Chi-restraints excluded: chain H residue  311 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 115 optimal weight:    0.8980
   chunk 208 optimal weight:    5.9990
   chunk 125 optimal weight:    0.8980
   chunk 220 optimal weight:    2.9990
   chunk 168 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 188 optimal weight:    9.9990
   chunk 195 optimal weight:    3.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 GLN
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 162 GLN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.141561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.121313 restraints weight = 32183.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122282 restraints weight = 26609.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.123851 restraints weight = 21252.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.123881 restraints weight = 15732.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.124711 restraints weight = 16324.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  19677  Z= 0.136
  Angle     :  0.656  14.078  26829  Z= 0.339
  Chirality :  0.044   0.358   3029
  Planarity :  0.004   0.055   3226
  Dihedral  : 14.362 169.989   3386
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.04 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.91 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -2.45 (0.17), residues: 2226
  helix: -0.29 (0.18), residues: 786
  sheet: -2.10 (0.26), residues: 348
  loop : -2.50 (0.17), residues: 1092

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 512 
 TYR   0.030   0.001   TYR E  64 
 PHE   0.034   0.001   PHE B  64 
 TRP   0.032   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (19674)
  covalent geometry    : angle       0.65641 (26829)
  hydrogen bonds       : bond        0.03361 (  630)
  hydrogen bonds       : angle       4.64811 ( 1777)
  metal coordination   : bond        0.00153 (    2)
  Misc. bond           : bond        0.00012 (    1)

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

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

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4452 Ramachandran restraints generated.
    2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 296
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A   37 ASP cc_start: 0.6651 (m-30) cc_final: 0.6423 (t0)
REVERT: A  351 LYS cc_start: 0.7308 (mmpt) cc_final: 0.6501 (tptt)
REVERT: A  728 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7993 (tp)
REVERT: C   38 SER cc_start: 0.8895 (m) cc_final: 0.8508 (p)
REVERT: G   64 TYR cc_start: 0.7336 (m-10) cc_final: 0.6749 (m-10)
REVERT: G  124 ASN cc_start: 0.8511 (p0) cc_final: 0.8144 (p0)
REVERT: G  164 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6981 (pm20)
REVERT: E  171 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6537 (mtp-110)
REVERT: B  219 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7871 (mt)
REVERT: H   43 MET cc_start: 0.8157 (mmm) cc_final: 0.7823 (mmt)
  outliers start: 52
  outliers final: 42
  residues processed: 331
  average time/residue: 0.1487
  time to fit residues: 76.1204
Evaluate side-chains
  334 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 288
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  570 SER
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain G residue   19 HIS
Chi-restraints excluded: chain G residue  132 GLU
Chi-restraints excluded: chain G residue  146 THR
Chi-restraints excluded: chain G residue  164 GLU
Chi-restraints excluded: chain G residue  180 ASP
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   80 SER
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  171 ARG
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  198 LEU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain H residue   15 LEU
Chi-restraints excluded: chain H residue   75 LEU
Chi-restraints excluded: chain H residue  173 LYS
Chi-restraints excluded: chain H residue  179 ASP
Chi-restraints excluded: chain H residue  199 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 227
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 156 optimal weight:    7.9990
   chunk 110 optimal weight:    0.8980
   chunk 185 optimal weight:    6.9990
   chunk 170 optimal weight:    0.5980
   chunk 146 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 115 optimal weight:    0.8980
   chunk 188 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 129 optimal weight:    3.9990
   overall best weight:    2.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
D  72 GLN
** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.138306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117927 restraints weight = 32386.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.118384 restraints weight = 27600.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.119966 restraints weight = 24006.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.119951 restraints weight = 17367.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.120397 restraints weight = 17797.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  19677  Z= 0.210
  Angle     :  0.706  12.871  26829  Z= 0.366
  Chirality :  0.046   0.379   3029
  Planarity :  0.004   0.054   3226
  Dihedral  : 14.441 170.815   3386
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.34 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 24.64 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -2.57 (0.17), residues: 2226
  helix: -0.42 (0.18), residues: 790
  sheet: -2.16 (0.26), residues: 347
  loop : -2.56 (0.17), residues: 1089

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 185 
 TYR   0.029   0.002   TYR E  64 
 PHE   0.038   0.002   PHE B  64 
 TRP   0.027   0.002   TRP A  38 
 HIS   0.004   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (19674)
  covalent geometry    : angle       0.70628 (26829)
  hydrogen bonds       : bond        0.03717 (  630)
  hydrogen bonds       : angle       4.82383 ( 1777)
  metal coordination   : bond        0.00271 (    2)
  Misc. bond           : bond        0.00005 (    1)

===============================================================================
Job complete
usr+sys time: 3012.15 seconds
wall clock time: 53 minutes 11.34 seconds (3191.34 seconds total)