Starting phenix.real_space_refine
on Sun Oct 25 08:56:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nea_49303/10_2026/9nea_49303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nea_49303/10_2026/9nea_49303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nea_49303/10_2026/9nea_49303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nea_49303/10_2026/9nea_49303.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nea_49303/10_2026/9nea_49303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nea_49303/10_2026/9nea_49303.map"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      57      5.49       5
     Mg      1      5.21       5
     S     103      5.16       5
     C   10318      2.51       5
     N    2795      2.21       5
     O    3300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16578
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 9375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1153, 9375
          Classifications: {'peptide': 1153}
          Link IDs: {'PTRANS': 58, 'TRANS': 1094}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "C"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "D"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "P"
      Number of atoms: 575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 575
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "T"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 595
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 9
          Unusual residues: {' MG': 1, 'SF4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5002  SG  CYS A 663      30.528  31.286  46.949  1.00 18.00           S
  ATOM   4936  SG  CYS A 654      28.282  37.530  45.698  1.00 18.61           S
  ATOM   4920  SG  CYS A 651      28.659  35.129  51.043  1.00 15.07           S

  Time building chain proxies: 3.52, per 1000 atoms: 0.21
  Number of scatterers: 16578
  At special positions: 0
  Unit cell: (105.156, 105.984, 148.212, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     S     103     16.00
     P      57     15.00
     Mg      1     11.99
     O    3300      8.00
     N    2795      7.00
     C   10318      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 735.6 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A2302 "
        pdb="FE2  SF4 A2302 " - pdb=" SG  CYS A 654 "
        pdb="FE1  SF4 A2302 " - pdb=" SG  CYS A 663 "
        pdb="FE4  SF4 A2302 " - pdb=" SG  CYS A 651 "
        pdb="FE3  SF4 A2302 " - pdb=" SG  CYS A 747 "
      Number of angles added : 12


  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3686

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 21 sheets defined
      34.6% alpha, 20.7% beta
      27 base pairs and 49 stacking pairs defined.
    Time for finding SS restraints: 2.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 48
      removed outlier: 3.532A  pdb=" N   ALA A  31 " --> pdb=" O   SER A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 124
      removed outlier: 3.546A  pdb=" N   SER A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 147
      removed outlier: 3.662A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 143 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY A 147 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 143 through 147'
    Processing helix  chain 'A' and resid 159 through 193
      Proline residue:  A 172  - end of helix
    Processing helix  chain 'A' and resid 227 through 236
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 367 through 379
      removed outlier: 3.556A  pdb=" N   PHE A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   HIS A 379 " --> pdb=" O   ARG A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 414
    Processing helix  chain 'A' and resid 418 through 422
      removed outlier: 4.002A  pdb=" N   HIS A 422 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 431
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.562A  pdb=" N   ASP A 443 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET A 444 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 440 through 444'
    Processing helix  chain 'A' and resid 451 through 473
      removed outlier: 3.645A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 451 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR A 473 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 483
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 496 through 512
    Processing helix  chain 'A' and resid 563 through 585
      removed outlier: 3.975A  pdb=" N   PHE A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   GLU A 575 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LYS A 576 " --> pdb=" O   GLN A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 593
      removed outlier: 3.555A  pdb=" N   VAL A 593 " --> pdb=" O   VAL A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 612
    Processing helix  chain 'A' and resid 629 through 639
      removed outlier: 3.777A  pdb=" N   ASN A 633 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 654
      removed outlier: 3.815A  pdb=" N   ALA A 653 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 4.152A  pdb=" N   GLU A 693 " --> pdb=" O   GLN A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 710
      removed outlier: 3.509A  pdb=" N   GLU A 709 " --> pdb=" O   ALA A 706 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LEU A 710 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 706 through 710'
    Processing helix  chain 'A' and resid 711 through 728
      removed outlier: 3.737A  pdb=" N   ASP A 725 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 786
    Processing helix  chain 'A' and resid 788 through 813
      removed outlier: 3.709A  pdb=" N   LYS A 792 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 821
      removed outlier: 3.978A  pdb=" N   ARG A 821 " --> pdb=" O   GLY A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 852
      removed outlier: 3.845A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 905
    Processing helix  chain 'A' and resid 979 through 992
      removed outlier: 4.353A  pdb=" N   LYS A 983 " --> pdb=" O   LEU A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1019
      removed outlier: 3.630A  pdb=" N   VAL A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1033
    Processing helix  chain 'A' and resid 1051 through 1062
    Processing helix  chain 'A' and resid 1066 through 1071
      removed outlier: 3.538A  pdb=" N   ASP A1071 " --> pdb=" O   GLN A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1097 through 1100
    Processing helix  chain 'A' and resid 1102 through 1113
    Processing helix  chain 'A' and resid 1123 through 1128
      removed outlier: 3.816A  pdb=" N   ILE A1127 " --> pdb=" O   ASP A1123 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU A1128 " --> pdb=" O   ILE A1124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1123 through 1128'
    Processing helix  chain 'A' and resid 1129 through 1145
    Processing helix  chain 'A' and resid 1145 through 1151
    Processing helix  chain 'A' and resid 1164 through 1175
      removed outlier: 3.909A  pdb=" N   ASN A1175 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 21
      removed outlier: 5.463A  pdb=" N   LEU B  16 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ASP B  21 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 57
      No H-bonds generated for 'chain 'B' and resid 55 through 57'
    Processing helix  chain 'B' and resid 72 through 79
    Processing helix  chain 'B' and resid 80 through 82
      No H-bonds generated for 'chain 'B' and resid 80 through 82'
    Processing helix  chain 'B' and resid 141 through 155
      removed outlier: 3.936A  pdb=" N   HIS B 153 " --> pdb=" O   ARG B 149 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ILE B 154 " --> pdb=" O   ASP B 150 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 216
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 4.399A  pdb=" N   LEU C  16 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 78
    Processing helix  chain 'C' and resid 141 through 152
      removed outlier: 4.213A  pdb=" N   ASP C 150 " --> pdb=" O   ARG C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.746A  pdb=" N   THR C 216 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 222
      Proline residue:  C 220  - end of helix
      No H-bonds generated for 'chain 'C' and resid 217 through 222'
    Processing helix  chain 'D' and resid 8 through 18
      removed outlier: 4.379A  pdb=" N   LEU D  12 " --> pdb=" O   GLN D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 81
    Processing helix  chain 'D' and resid 141 through 155
      removed outlier: 3.895A  pdb=" N   ASP D 150 " --> pdb=" O   ARG D 146 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS D 153 " --> pdb=" O   ARG D 149 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ILE D 154 " --> pdb=" O   ASP D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 194
    Processing helix  chain 'D' and resid 209 through 216
    Processing helix  chain 'D' and resid 217 through 219
      No H-bonds generated for 'chain 'D' and resid 217 through 219'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52
      removed outlier: 5.696A  pdb=" N   GLU A  51 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ALA A  97 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52
      removed outlier: 5.696A  pdb=" N   GLU A  51 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ALA A  97 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   TYR A  85 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TRP A 243 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 136
      removed outlier: 3.550A  pdb=" N   GLU A 132 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A 150 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ASN A 151 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   THR A 108 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 104 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TYR A 105 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ASP A 220 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 295 through 300
      removed outlier: 3.681A  pdb=" N   GLU A 337 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 361
    Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 391
      removed outlier: 3.977A  pdb=" N   LYS A 398 " --> pdb=" O   GLN A 390 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 538
      removed outlier: 3.809A  pdb=" N   SER A 536 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 665 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 553
      removed outlier: 4.368A  pdb=" N   ALA A 939 " --> pdb=" O   PHE A 959 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   TYR A 956 " --> pdb=" O   LYS A 969 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   LYS A 969 " --> pdb=" O   TYR A 956 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 561
    Processing sheet with id=AB1, first strand: chain 'A' and resid 620 through 625
      removed outlier: 5.620A  pdb=" N   VAL A 867 " --> pdb=" O   PRO A 856 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 911 through 915
      removed outlier: 6.898A  pdb=" N   THR A 920 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1035 through 1039
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1189 through 1191
      removed outlier: 4.081A  pdb=" N   GLY A1191 " --> pdb=" O   GLN D 125 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLN D 125 " --> pdb=" O   GLY A1191 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 2 through 6
      removed outlier: 3.845A  pdb=" N   PHE B 103 " --> pdb=" O   SER B 112 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL B 111 " --> pdb=" O   LYS C 181 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY C 178 " --> pdb=" O   ALA C 171 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE C 180 " --> pdb=" O   PHE C 169 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 182 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 68
      removed outlier: 5.326A  pdb=" N   SER B 230 " --> pdb=" O   PRO B 234 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR B 226 " --> pdb=" O   GLU B 238 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 208
      removed outlier: 3.548A  pdb=" N   VAL D 111 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 66 through 68
      removed outlier: 4.428A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 110 through 112
    Processing sheet with id=AC1, first strand: chain 'C' and resid 110 through 112
      removed outlier: 4.878A  pdb=" N   VAL D 167 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA D 157 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 39 through 40
      removed outlier: 4.326A  pdb=" N   SER D  39 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   VAL D  48 " --> pdb=" O   SER D  39 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU D  50 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 39 through 40
      removed outlier: 4.326A  pdb=" N   SER D  39 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   VAL D  48 " --> pdb=" O   SER D  39 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   LYS D 240 " --> pdb=" O   THR D 224 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   THR D 224 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)

    699 hydrogen bonds defined for protein.
    1965 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      64 hydrogen bonds
      128 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      49 stacking parallelities
  Total time for adding SS restraints: 4.75

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.17 -     1.39: 6741
        1.39 -     1.61: 10102
        1.61 -     1.84: 163
        1.84 -     2.06: 0
        2.06 -     2.28: 13
  Bond restraints: 17019
  Sorted by residual:
  bond pdb=" C4' PST P  35 "
       pdb=" O4' PST P  35 "
    ideal  model  delta    sigma   weight residual
    1.420  1.667 -0.247 2.00e-02 2.50e+03 1.52e+02
  bond pdb=" C4' PST P  35 "
       pdb=" C3' PST P  35 "
    ideal  model  delta    sigma   weight residual
    1.525  1.339  0.186 2.00e-02 2.50e+03 8.69e+01
  bond pdb=" P   PST P  35 "
       pdb=" SP  PST P  35 "
    ideal  model  delta    sigma   weight residual
    1.925  2.106 -0.181 2.00e-02 2.50e+03 8.19e+01
  bond pdb=" O4' PST P  35 "
       pdb=" C1' PST P  35 "
    ideal  model  delta    sigma   weight residual
    1.400  1.305  0.095 2.00e-02 2.50e+03 2.28e+01
  bond pdb=" C4  PST P  35 "
       pdb=" C5  PST P  35 "
    ideal  model  delta    sigma   weight residual
    1.448  1.355  0.093 2.00e-02 2.50e+03 2.14e+01
  ... (remaining 17014 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.63: 23221
        7.63 -    15.26: 21
       15.26 -    22.89: 0
       22.89 -    30.53: 0
       30.53 -    38.16: 1
  Bond angle restraints: 23243
  Sorted by residual:
  angle pdb=" O3'  DA P  34 "
        pdb=" P   PST P  35 "
        pdb=" O5' PST P  35 "
      ideal   model   delta    sigma   weight residual
     104.00  142.16  -38.16 1.90e+00 2.77e-01 4.03e+02
  angle pdb=" C3'  DA P  34 "
        pdb=" O3'  DA P  34 "
        pdb=" P   PST P  35 "
      ideal   model   delta    sigma   weight residual
     119.70  131.86  -12.16 1.20e+00 6.94e-01 1.03e+02
  angle pdb=" N   VAL A1069 "
        pdb=" CA  VAL A1069 "
        pdb=" C   VAL A1069 "
      ideal   model   delta    sigma   weight residual
     112.96  107.74    5.22 1.00e+00 1.00e+00 2.73e+01
  angle pdb=" C   PRO A 856 "
        pdb=" CA  PRO A 856 "
        pdb=" CB  PRO A 856 "
      ideal   model   delta    sigma   weight residual
     111.56  119.23   -7.67 1.65e+00 3.67e-01 2.16e+01
  angle pdb=" C   SER D 134 "
        pdb=" N   CYS D 135 "
        pdb=" CA  CYS D 135 "
      ideal   model   delta    sigma   weight residual
     122.99  116.46    6.53 1.41e+00 5.03e-01 2.14e+01
  ... (remaining 23238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 8894
       17.88 -    35.76: 971
       35.76 -    53.64: 329
       53.64 -    71.52: 71
       71.52 -    89.40: 14
  Dihedral angle restraints: 10279
    sinusoidal: 4592
      harmonic: 5687
  Sorted by residual:
  dihedral pdb=" CA  GLU B 198 "
           pdb=" C   GLU B 198 "
           pdb=" N   MET B 199 "
           pdb=" CA  MET B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.07  -29.93     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  ARG A 413 "
           pdb=" C   ARG A 413 "
           pdb=" N   ASP A 414 "
           pdb=" CA  ASP A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.14  -28.86     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ASN A 751 "
           pdb=" C   ASN A 751 "
           pdb=" N   SER A 752 "
           pdb=" CA  SER A 752 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.10   26.90     0      5.00e+00 4.00e-02 2.89e+01
  ... (remaining 10276 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 2480
       0.110 -    0.220: 109
       0.220 -    0.330: 2
       0.330 -    0.440: 0
       0.440 -    0.550: 1
  Chirality restraints: 2592
  Sorted by residual:
  chirality pdb=" P    DA T   8 "
            pdb=" OP1  DA T   8 "
            pdb=" OP2  DA T   8 "
            pdb=" O5'  DA T   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.89   -0.55 2.00e-01 2.50e+01 7.56e+00
  chirality pdb=" CB  VAL A 240 "
            pdb=" CA  VAL A 240 "
            pdb=" CG1 VAL A 240 "
            pdb=" CG2 VAL A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C4' PST P  35 "
            pdb=" C5' PST P  35 "
            pdb=" O4' PST P  35 "
            pdb=" C3' PST P  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.61    0.24 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 2589 not shown)

  Planarity restraints: 2798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 811 "    0.016 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   ILE A 811 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   ILE A 811 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU A 812 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 722 "    0.258 9.50e-02 1.11e+02   1.16e-01 8.82e+00
        pdb=" NE  ARG A 722 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 722 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 722 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 722 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 250 "   -0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   TYR C 250 "    0.046 2.00e-02 2.50e+03
        pdb=" O   TYR C 250 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU C 251 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2795 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 28
        2.63 -     3.20: 14324
        3.20 -     3.76: 27225
        3.76 -     4.33: 35565
        4.33 -     4.90: 56482
  Nonbonded interactions: 133624
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 275 "
            pdb="MG    MG A2301 "
     model   vdw
     2.059 2.170
  nonbonded pdb=" O4' PST P  35 "
            pdb=" C6  PST P  35 "
     model   vdw
     2.523 2.672
  nonbonded pdb=" O   ASN A 662 "
            pdb=" ND2 ASN A 662 "
     model   vdw
     2.527 3.120
  nonbonded pdb=" CA  CYS A 747 "
            pdb="FE3  SF4 A2302 "
     model   vdw
     2.537 2.744
  nonbonded pdb=" O   THR A 757 "
            pdb=" CB  PHE A 761 "
     model   vdw
     2.539 2.752
  ... (remaining 133619 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 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     21.430
  Find NCS groups from input model:        0.270
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5857
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   0.913  17023  Z= 0.383
  Angle     :  1.081  45.557  23255  Z= 0.543
  Chirality :  0.054   0.550   2592
  Planarity :  0.006   0.116   2798
  Dihedral  : 17.222  89.397   6593
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.41 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.18), residues: 1926
  helix: -1.09 (0.20), residues: 592
  sheet: -0.90 (0.24), residues: 452
  loop : -1.99 (0.19), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 722 
 TYR   0.027   0.002   TYR A 623 
 PHE   0.034   0.003   PHE A 815 
 TRP   0.009   0.001   TRP A 369 
 HIS   0.020   0.002   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00579 /  0.32 (17019)
  covalent geometry    : angle       0.94358 /  0.54 (23243)
  hydrogen bonds       : bond        0.11543 /  7.17 (  755)
  hydrogen bonds       : angle       6.59555 /  4.63 ( 2093)
  metal coordination   : bond        0.45628 / 22.81 (    4)
  metal coordination   : angle      23.25414 / 15.18 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.6956 (pttp) cc_final: 0.6696 (ptpt)
REVERT: A  294 MET cc_start: 0.6038 (pmm) cc_final: 0.5561 (pmm)
REVERT: A  295 MET cc_start: 0.6444 (ttm) cc_final: 0.5697 (ttp)
REVERT: A  381 LEU cc_start: 0.6623 (mp) cc_final: 0.6329 (mp)
REVERT: A  584 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7115 (mm-30)
REVERT: A  687 GLN cc_start: 0.7113 (pp30) cc_final: 0.6707 (tt0)
REVERT: A 1168 HIS cc_start: 0.5849 (t70) cc_final: 0.5548 (t-170)
REVERT: B   95 ASN cc_start: 0.6297 (t0) cc_final: 0.5919 (t0)
REVERT: B  213 ASN cc_start: 0.7748 (t0) cc_final: 0.7433 (t0)
REVERT: D  133 TYR cc_start: 0.5932 (m-80) cc_final: 0.5454 (m-80)
REVERT: D  199 MET cc_start: 0.3038 (mmt) cc_final: 0.2556 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 276
  average time/residue: 0.1250
  time to fit residues: 51.9656
Evaluate side-chains
  200 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  747 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 77, 122, 91]
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 ASN
A 662 ASN
A 670 GLN
A 852 GLN
C  71 ASN
C 246 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.211966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.184296 restraints weight = 25586.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.184237 restraints weight = 29975.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.185718 restraints weight = 25075.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.186034 restraints weight = 18316.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.186352 restraints weight = 18172.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5952
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  17023  Z= 0.197
  Angle     :  0.910  54.554  23255  Z= 0.369
  Chirality :  0.046   0.210   2592
  Planarity :  0.005   0.071   2798
  Dihedral  : 17.034  67.361   2749
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.62 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.18), residues: 1926
  helix: -0.62 (0.21), residues: 602
  sheet: -0.86 (0.24), residues: 447
  loop : -1.86 (0.19), residues: 877

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1160 
 TYR   0.018   0.002   TYR A 623 
 PHE   0.035   0.002   PHE A 569 
 TRP   0.010   0.001   TRP A 369 
 HIS   0.013   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.20 (17019)
  covalent geometry    : angle       0.69313 /  0.37 (23243)
  hydrogen bonds       : bond        0.04550 /  2.93 (  755)
  hydrogen bonds       : angle       5.60423 /  3.99 ( 2093)
  metal coordination   : bond        0.01633 /  0.81 (    4)
  metal coordination   : angle      25.95099 / 17.40 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 206
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 MET cc_start: 0.5937 (pmm) cc_final: 0.5504 (pmm)
REVERT: A  295 MET cc_start: 0.6277 (ttm) cc_final: 0.5953 (ttp)
REVERT: A  414 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6527 (t70)
REVERT: A  584 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6894 (mm-30)
REVERT: A  606 LYS cc_start: 0.6218 (pttt) cc_final: 0.5736 (tttp)
REVERT: A  687 GLN cc_start: 0.7067 (pp30) cc_final: 0.6659 (tt0)
REVERT: A 1013 TRP cc_start: 0.4183 (m100) cc_final: 0.3873 (t-100)
REVERT: A 1168 HIS cc_start: 0.5791 (t70) cc_final: 0.5567 (t-170)
REVERT: B   95 ASN cc_start: 0.6890 (t0) cc_final: 0.6475 (t0)
REVERT: B  213 ASN cc_start: 0.7939 (t0) cc_final: 0.7613 (t0)
REVERT: C   40 MET cc_start: 0.4511 (pmm) cc_final: 0.3910 (pmm)
REVERT: D   49 GLN cc_start: 0.4789 (pm20) cc_final: 0.4316 (pm20)
REVERT: D  133 TYR cc_start: 0.5818 (m-80) cc_final: 0.5467 (m-80)
REVERT: D  199 MET cc_start: 0.2799 (mmt) cc_final: 0.2393 (mmm)
  outliers start: 19
  outliers final: 15
  residues processed: 219
  average time/residue: 0.1235
  time to fit residues: 41.1007
Evaluate side-chains
  207 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 191
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   71 ASN
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [70, 183, 112, 38, 140, 34, 154, 153, 86, 172, 73]
   chunk 70 optimal weight:    0.5980
   chunk 183 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 140 optimal weight:    0.2980
   chunk 34 optimal weight:    3.9990
   chunk 154 optimal weight:    0.0980
   chunk 153 optimal weight:   20.0000
   chunk 86 optimal weight:    0.8980
   chunk 172 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
** C  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 246 HIS
D 200 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.217577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.188079 restraints weight = 25565.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.188575 restraints weight = 24643.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.190909 restraints weight = 19965.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.190820 restraints weight = 14977.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.190970 restraints weight = 15341.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5951
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17023  Z= 0.124
  Angle     :  0.835  50.123  23255  Z= 0.329
  Chirality :  0.044   0.187   2592
  Planarity :  0.004   0.058   2798
  Dihedral  : 16.876  66.612   2748
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.02 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.18), residues: 1926
  helix: -0.32 (0.21), residues: 606
  sheet: -0.72 (0.24), residues: 453
  loop : -1.81 (0.19), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 559 
 TYR   0.014   0.001   TYR A 623 
 PHE   0.021   0.002   PHE A 596 
 TRP   0.009   0.001   TRP A 671 
 HIS   0.013   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (17019)
  covalent geometry    : angle       0.61827 /  0.33 (23243)
  hydrogen bonds       : bond        0.03926 /  2.54 (  755)
  hydrogen bonds       : angle       5.33477 /  3.82 ( 2093)
  metal coordination   : bond        0.00949 /  0.47 (    4)
  metal coordination   : angle      24.68966 / 16.35 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 205
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 MET cc_start: 0.6275 (ttm) cc_final: 0.5825 (ttp)
REVERT: A  414 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.6340 (t70)
REVERT: A  606 LYS cc_start: 0.6320 (pttt) cc_final: 0.5762 (tttp)
REVERT: A  687 GLN cc_start: 0.7243 (pp30) cc_final: 0.6756 (tt0)
REVERT: A  831 MET cc_start: 0.6609 (mtt) cc_final: 0.6288 (mtt)
REVERT: A  900 MET cc_start: 0.7099 (ppp) cc_final: 0.6244 (ppp)
REVERT: A 1013 TRP cc_start: 0.4289 (m100) cc_final: 0.3766 (t-100)
REVERT: A 1168 HIS cc_start: 0.5951 (t70) cc_final: 0.5680 (t-170)
REVERT: B   95 ASN cc_start: 0.7156 (t0) cc_final: 0.6734 (t0)
REVERT: B  213 ASN cc_start: 0.7796 (t0) cc_final: 0.7484 (t0)
REVERT: C   40 MET cc_start: 0.4264 (pmm) cc_final: 0.3763 (pmm)
REVERT: D  116 MET cc_start: 0.1174 (tpp) cc_final: 0.0621 (tpp)
  outliers start: 15
  outliers final: 10
  residues processed: 217
  average time/residue: 0.1169
  time to fit residues: 39.1995
Evaluate side-chains
  196 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 185
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [16, 147, 85, 115, 34, 40, 118, 87, 188, 12, 89]
   chunk 16 optimal weight:   20.0000
   chunk 147 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 115 optimal weight:    0.0980
   chunk 34 optimal weight:    5.9990
   chunk 40 optimal weight:    0.3980
   chunk 118 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   chunk 188 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 ASN
C  71 ASN
C 246 HIS
D 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.211635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.184779 restraints weight = 25635.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.184756 restraints weight = 32200.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.186002 restraints weight = 28728.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.186645 restraints weight = 20825.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.186880 restraints weight = 19607.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5954
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  17023  Z= 0.149
  Angle     :  0.844  51.935  23255  Z= 0.328
  Chirality :  0.043   0.175   2592
  Planarity :  0.004   0.058   2798
  Dihedral  : 16.876  65.661   2748
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.72 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.18), residues: 1926
  helix: -0.15 (0.21), residues: 606
  sheet: -0.70 (0.24), residues: 442
  loop : -1.74 (0.20), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 559 
 TYR   0.015   0.002   TYR A 362 
 PHE   0.020   0.002   PHE D 207 
 TRP   0.009   0.001   TRP A 369 
 HIS   0.010   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 (17019)
  covalent geometry    : angle       0.61948 /  0.32 (23243)
  hydrogen bonds       : bond        0.03893 /  2.53 (  755)
  hydrogen bonds       : angle       5.17187 /  3.69 ( 2093)
  metal coordination   : bond        0.01267 /  0.63 (    4)
  metal coordination   : angle      25.27345 / 16.83 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 MET cc_start: 0.6411 (ttm) cc_final: 0.5832 (ttp)
REVERT: A  425 LYS cc_start: 0.6502 (mttm) cc_final: 0.6217 (mptt)
REVERT: A  606 LYS cc_start: 0.6315 (pttt) cc_final: 0.5776 (tttp)
REVERT: A  687 GLN cc_start: 0.7263 (pp30) cc_final: 0.6732 (tt0)
REVERT: A  900 MET cc_start: 0.6995 (ppp) cc_final: 0.6160 (ppp)
REVERT: A 1013 TRP cc_start: 0.4376 (m100) cc_final: 0.3872 (t-100)
REVERT: A 1168 HIS cc_start: 0.5867 (t70) cc_final: 0.5578 (t-170)
REVERT: B  156 ASP cc_start: 0.6773 (m-30) cc_final: 0.5873 (t70)
REVERT: B  213 ASN cc_start: 0.7841 (t0) cc_final: 0.7603 (t0)
REVERT: C   40 MET cc_start: 0.4353 (pmm) cc_final: 0.4022 (pmm)
REVERT: D  116 MET cc_start: 0.1313 (tpp) cc_final: 0.0929 (tpp)
  outliers start: 30
  outliers final: 22
  residues processed: 219
  average time/residue: 0.1163
  time to fit residues: 39.4565
Evaluate side-chains
  213 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   71 ASN
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   24 ASN
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [8, 114, 55, 120, 151, 102, 127, 95, 35, 105, 89]
   chunk 8 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 120 optimal weight:    5.9990
   chunk 151 optimal weight:    0.5980
   chunk 102 optimal weight:    6.9990
   chunk 127 optimal weight:   30.0000
   chunk 95 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    3.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 ASN
C 246 HIS
** D  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.205741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.179986 restraints weight = 25015.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.178638 restraints weight = 37426.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.179452 restraints weight = 32801.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.180011 restraints weight = 25198.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.180290 restraints weight = 22925.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6201
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.109  17023  Z= 0.312
  Angle     :  1.044  59.581  23255  Z= 0.423
  Chirality :  0.050   0.266   2592
  Planarity :  0.006   0.062   2798
  Dihedral  : 17.156  65.286   2748
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 19.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.54 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.18), residues: 1926
  helix: -0.59 (0.20), residues: 607
  sheet: -1.04 (0.23), residues: 444
  loop : -2.00 (0.19), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 722 
 TYR   0.019   0.003   TYR A 827 
 PHE   0.034   0.003   PHE A 761 
 TRP   0.010   0.002   TRP B  28 
 HIS   0.015   0.002   HIS C 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00735 /  0.31 (17019)
  covalent geometry    : angle       0.79457 /  0.42 (23243)
  hydrogen bonds       : bond        0.04913 /  3.21 (  755)
  hydrogen bonds       : angle       5.61208 /  3.99 ( 2093)
  metal coordination   : bond        0.04781 /  2.39 (    4)
  metal coordination   : angle      29.81696 / 19.91 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 205
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6624 (ttp80)
REVERT: A  295 MET cc_start: 0.6743 (ttm) cc_final: 0.6108 (ttp)
REVERT: A  425 LYS cc_start: 0.6715 (mttm) cc_final: 0.6401 (mptt)
REVERT: A  606 LYS cc_start: 0.6265 (pttt) cc_final: 0.5713 (tttp)
REVERT: A  687 GLN cc_start: 0.7429 (pp30) cc_final: 0.6826 (tt0)
REVERT: A  831 MET cc_start: 0.7090 (ttm) cc_final: 0.6727 (ttm)
REVERT: A  900 MET cc_start: 0.7108 (ppp) cc_final: 0.6307 (ppp)
REVERT: A 1091 GLU cc_start: 0.8064 (tp30) cc_final: 0.7782 (tp30)
REVERT: B   68 MET cc_start: 0.2820 (tmm) cc_final: 0.1116 (mmt)
REVERT: B  119 MET cc_start: 0.2198 (pmm) cc_final: 0.1707 (pmm)
REVERT: B  156 ASP cc_start: 0.6860 (m-30) cc_final: 0.6127 (t70)
REVERT: B  213 ASN cc_start: 0.8022 (t0) cc_final: 0.7698 (t0)
  outliers start: 44
  outliers final: 36
  residues processed: 237
  average time/residue: 0.1210
  time to fit residues: 43.8833
Evaluate side-chains
  236 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 200
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   71 ASN
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [52, 191, 176, 146, 139, 56, 53, 187, 43, 113, 22]
   chunk 52 optimal weight:    0.9980
   chunk 191 optimal weight:    0.9980
   chunk 176 optimal weight:    5.9990
   chunk 146 optimal weight:    5.9990
   chunk 139 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 187 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 748 GLN
** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.208512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.179054 restraints weight = 25150.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.178571 restraints weight = 31138.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.180837 restraints weight = 25032.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.180847 restraints weight = 19262.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.181453 restraints weight = 19488.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.4508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17023  Z= 0.139
  Angle     :  0.884  48.693  23255  Z= 0.341
  Chirality :  0.045   0.191   2592
  Planarity :  0.004   0.067   2798
  Dihedral  : 16.917  65.880   2748
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.59 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.18), residues: 1926
  helix: -0.31 (0.21), residues: 608
  sheet: -0.96 (0.23), residues: 449
  loop : -1.79 (0.20), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 705 
 TYR   0.015   0.002   TYR A 892 
 PHE   0.026   0.002   PHE D 207 
 TRP   0.016   0.001   TRP A 671 
 HIS   0.009   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 (17019)
  covalent geometry    : angle       0.64823 /  0.34 (23243)
  hydrogen bonds       : bond        0.03829 /  2.50 (  755)
  hydrogen bonds       : angle       5.27546 /  3.78 ( 2093)
  metal coordination   : bond        0.00889 /  0.44 (    4)
  metal coordination   : angle      26.48660 / 16.99 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 206
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.6939 (ttp80) cc_final: 0.6585 (ttp80)
REVERT: A  295 MET cc_start: 0.6604 (ttm) cc_final: 0.5824 (ttp)
REVERT: A  425 LYS cc_start: 0.6564 (mttm) cc_final: 0.6265 (mptt)
REVERT: A  506 MET cc_start: 0.7158 (mmt) cc_final: 0.6111 (mmt)
REVERT: A  606 LYS cc_start: 0.6025 (pttt) cc_final: 0.5639 (tttp)
REVERT: A  687 GLN cc_start: 0.7460 (pp30) cc_final: 0.6780 (tt0)
REVERT: A  862 ASP cc_start: 0.6143 (t0) cc_final: 0.5706 (t0)
REVERT: A  900 MET cc_start: 0.7025 (ppp) cc_final: 0.6280 (ppp)
REVERT: B   68 MET cc_start: 0.2581 (tmm) cc_final: 0.1010 (mmt)
REVERT: B  119 MET cc_start: 0.2372 (pmm) cc_final: 0.2021 (pmm)
REVERT: B  147 ILE cc_start: 0.6142 (OUTLIER) cc_final: 0.5498 (tp)
REVERT: B  156 ASP cc_start: 0.6763 (m-30) cc_final: 0.5533 (t70)
REVERT: B  213 ASN cc_start: 0.7909 (t0) cc_final: 0.7624 (t0)
REVERT: D  116 MET cc_start: 0.1555 (tpp) cc_final: 0.1277 (tpp)
  outliers start: 34
  outliers final: 25
  residues processed: 231
  average time/residue: 0.1231
  time to fit residues: 44.0441
Evaluate side-chains
  223 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [102, 51, 71, 118, 88, 86, 167, 162, 81, 122, 38]
   chunk 102 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 118 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 167 optimal weight:    9.9990
   chunk 162 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 ASN
C  71 ASN
C 246 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.208337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.181685 restraints weight = 25148.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.181387 restraints weight = 32463.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.183112 restraints weight = 26415.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.183330 restraints weight = 20586.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.183816 restraints weight = 20834.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6035
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  17023  Z= 0.142
  Angle     :  0.870  48.679  23255  Z= 0.332
  Chirality :  0.044   0.185   2592
  Planarity :  0.004   0.057   2798
  Dihedral  : 16.826  64.947   2748
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.47 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.18), residues: 1926
  helix: -0.11 (0.21), residues: 601
  sheet: -0.94 (0.24), residues: 445
  loop : -1.68 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 847 
 TYR   0.014   0.002   TYR A 623 
 PHE   0.025   0.002   PHE D 207 
 TRP   0.016   0.002   TRP A 671 
 HIS   0.007   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 (17019)
  covalent geometry    : angle       0.63057 /  0.33 (23243)
  hydrogen bonds       : bond        0.03819 /  2.48 (  755)
  hydrogen bonds       : angle       5.15901 /  3.69 ( 2093)
  metal coordination   : bond        0.01066 /  0.53 (    4)
  metal coordination   : angle      26.36548 / 17.01 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 200
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.6819 (ttp80) cc_final: 0.6520 (ttp80)
REVERT: A  295 MET cc_start: 0.6569 (ttm) cc_final: 0.5866 (ttp)
REVERT: A  425 LYS cc_start: 0.6595 (mttm) cc_final: 0.6249 (mptt)
REVERT: A  583 GLU cc_start: 0.6635 (pt0) cc_final: 0.6410 (tp30)
REVERT: A  606 LYS cc_start: 0.6001 (pttt) cc_final: 0.5599 (tttp)
REVERT: A  687 GLN cc_start: 0.7394 (pp30) cc_final: 0.6770 (tt0)
REVERT: A  862 ASP cc_start: 0.6122 (t0) cc_final: 0.5677 (t0)
REVERT: A  900 MET cc_start: 0.6965 (ppp) cc_final: 0.6183 (ppp)
REVERT: A 1091 GLU cc_start: 0.8010 (tp30) cc_final: 0.7756 (tp30)
REVERT: B   68 MET cc_start: 0.2483 (tmm) cc_final: 0.0980 (mmt)
REVERT: B  119 MET cc_start: 0.2375 (pmm) cc_final: 0.2072 (pmm)
REVERT: B  147 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5468 (tp)
REVERT: B  156 ASP cc_start: 0.6730 (m-30) cc_final: 0.5547 (t70)
REVERT: B  213 ASN cc_start: 0.7907 (t0) cc_final: 0.7626 (t0)
REVERT: C   40 MET cc_start: 0.4573 (pmm) cc_final: 0.3951 (pmm)
REVERT: D  116 MET cc_start: 0.1741 (tpp) cc_final: 0.1538 (tpp)
  outliers start: 36
  outliers final: 32
  residues processed: 227
  average time/residue: 0.1193
  time to fit residues: 41.8070
Evaluate side-chains
  223 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   71 ASN
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [38, 174, 80, 190, 192, 79, 142, 141, 65, 195, 112]
   chunk 38 optimal weight:    3.9990
   chunk 174 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 190 optimal weight:    0.8980
   chunk 192 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 142 optimal weight:    0.8980
   chunk 141 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 195 optimal weight:   30.0000
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 ASN
C  71 ASN
C 246 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.212930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.184214 restraints weight = 24813.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.184465 restraints weight = 25370.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.186094 restraints weight = 21295.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.185989 restraints weight = 17196.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.186410 restraints weight = 15044.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6074
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  17023  Z= 0.132
  Angle     :  0.862  47.402  23255  Z= 0.331
  Chirality :  0.044   0.187   2592
  Planarity :  0.004   0.056   2798
  Dihedral  : 16.757  64.751   2748
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.71 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.19), residues: 1926
  helix: -0.03 (0.21), residues: 598
  sheet: -0.79 (0.24), residues: 443
  loop : -1.63 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 847 
 TYR   0.014   0.001   TYR A 623 
 PHE   0.037   0.002   PHE A1109 
 TRP   0.020   0.001   TRP A1013 
 HIS   0.016   0.001   HIS C 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 (17019)
  covalent geometry    : angle       0.63321 /  0.33 (23243)
  hydrogen bonds       : bond        0.03696 /  2.40 (  755)
  hydrogen bonds       : angle       5.06629 /  3.62 ( 2093)
  metal coordination   : bond        0.00811 /  0.40 (    4)
  metal coordination   : angle      25.76535 / 16.56 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 199
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.6902 (ttp80) cc_final: 0.6570 (ttp80)
REVERT: A  295 MET cc_start: 0.6559 (ttm) cc_final: 0.5876 (ttp)
REVERT: A  425 LYS cc_start: 0.6633 (mttm) cc_final: 0.6230 (mptt)
REVERT: A  606 LYS cc_start: 0.6061 (pttt) cc_final: 0.5638 (tttp)
REVERT: A  687 GLN cc_start: 0.7455 (pp30) cc_final: 0.6778 (tt0)
REVERT: A  900 MET cc_start: 0.6979 (ppp) cc_final: 0.6137 (ppp)
REVERT: A 1091 GLU cc_start: 0.8000 (tp30) cc_final: 0.7785 (tp30)
REVERT: B  147 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5460 (tp)
REVERT: B  156 ASP cc_start: 0.6720 (m-30) cc_final: 0.5523 (t70)
REVERT: B  213 ASN cc_start: 0.7868 (t0) cc_final: 0.7603 (t0)
REVERT: C   40 MET cc_start: 0.4577 (pmm) cc_final: 0.4120 (pmm)
REVERT: C   91 ARG cc_start: 0.3768 (ptm160) cc_final: 0.2833 (ptm160)
  outliers start: 40
  outliers final: 32
  residues processed: 232
  average time/residue: 0.1177
  time to fit residues: 42.2044
Evaluate side-chains
  226 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 193
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   24 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [44, 70, 77, 126, 92, 100, 68, 96, 98, 175, 131]
   chunk 44 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 77 optimal weight:    0.4980
   chunk 126 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 96 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 175 optimal weight:    7.9990
   chunk 131 optimal weight:    0.0970
   overall best weight:    0.4978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 808 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.211395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.183306 restraints weight = 25153.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.183983 restraints weight = 28407.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.185603 restraints weight = 23369.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.185795 restraints weight = 17540.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.186121 restraints weight = 17549.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5986
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17023  Z= 0.124
  Angle     :  0.855  45.740  23255  Z= 0.333
  Chirality :  0.043   0.180   2592
  Planarity :  0.004   0.055   2798
  Dihedral  : 16.685  64.578   2748
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.41 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.19), residues: 1926
  helix:  0.02 (0.21), residues: 599
  sheet: -0.66 (0.24), residues: 452
  loop : -1.61 (0.20), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 722 
 TYR   0.018   0.001   TYR A 100 
 PHE   0.028   0.002   PHE A1109 
 TRP   0.019   0.001   TRP A 671 
 HIS   0.010   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 (17019)
  covalent geometry    : angle       0.64411 /  0.33 (23243)
  hydrogen bonds       : bond        0.03643 /  2.36 (  755)
  hydrogen bonds       : angle       4.98877 /  3.57 ( 2093)
  metal coordination   : bond        0.00779 /  0.38 (    4)
  metal coordination   : angle      24.77529 / 15.86 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 202
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 MET cc_start: 0.6489 (ttm) cc_final: 0.5865 (ttp)
REVERT: A  425 LYS cc_start: 0.6653 (mttm) cc_final: 0.6212 (mptt)
REVERT: A  583 GLU cc_start: 0.6688 (pt0) cc_final: 0.6424 (tp30)
REVERT: A  606 LYS cc_start: 0.6083 (pttt) cc_final: 0.5655 (tttp)
REVERT: A  687 GLN cc_start: 0.7362 (pp30) cc_final: 0.6720 (tt0)
REVERT: A  900 MET cc_start: 0.6884 (ppp) cc_final: 0.6020 (ppp)
REVERT: A 1091 GLU cc_start: 0.7960 (tp30) cc_final: 0.7751 (tp30)
REVERT: B  147 ILE cc_start: 0.6047 (OUTLIER) cc_final: 0.5406 (tp)
REVERT: B  156 ASP cc_start: 0.6577 (m-30) cc_final: 0.5663 (t70)
REVERT: B  213 ASN cc_start: 0.7868 (t0) cc_final: 0.7583 (t0)
REVERT: C   40 MET cc_start: 0.4584 (pmm) cc_final: 0.4186 (pmm)
  outliers start: 37
  outliers final: 33
  residues processed: 234
  average time/residue: 0.1192
  time to fit residues: 43.0815
Evaluate side-chains
  230 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   24 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  224 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [162, 55, 171, 50, 46, 64, 2, 125, 194, 1, 85]
   chunk 162 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 171 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 125 optimal weight:    6.9990
   chunk 194 optimal weight:   20.0000
   chunk 1 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.214214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.185332 restraints weight = 24898.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.186382 restraints weight = 25466.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.188456 restraints weight = 21023.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.187762 restraints weight = 18442.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.188801 restraints weight = 15904.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6017
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17023  Z= 0.130
  Angle     :  0.868  45.950  23255  Z= 0.337
  Chirality :  0.044   0.209   2592
  Planarity :  0.004   0.055   2798
  Dihedral  : 16.660  64.160   2748
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.70 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.19), residues: 1926
  helix:  0.04 (0.21), residues: 599
  sheet: -0.70 (0.24), residues: 459
  loop : -1.60 (0.20), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 722 
 TYR   0.017   0.002   TYR C 249 
 PHE   0.026   0.002   PHE A1109 
 TRP   0.017   0.001   TRP A 671 
 HIS   0.005   0.001   HIS A 772 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 (17019)
  covalent geometry    : angle       0.65943 /  0.33 (23243)
  hydrogen bonds       : bond        0.03644 /  2.37 (  755)
  hydrogen bonds       : angle       4.98176 /  3.56 ( 2093)
  metal coordination   : bond        0.00793 /  0.39 (    4)
  metal coordination   : angle      24.88218 / 16.00 (   12)

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

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

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3852 Ramachandran restraints generated.
    1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 198
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 MET cc_start: 0.6510 (ttm) cc_final: 0.5879 (ttp)
REVERT: A  425 LYS cc_start: 0.6676 (mttm) cc_final: 0.6212 (mptt)
REVERT: A  583 GLU cc_start: 0.6735 (pt0) cc_final: 0.6451 (tp30)
REVERT: A  606 LYS cc_start: 0.6107 (pttt) cc_final: 0.5664 (tttp)
REVERT: A  900 MET cc_start: 0.6877 (ppp) cc_final: 0.6009 (ppp)
REVERT: A 1091 GLU cc_start: 0.7956 (tp30) cc_final: 0.7752 (tp30)
REVERT: B  147 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5415 (tp)
REVERT: B  156 ASP cc_start: 0.6684 (m-30) cc_final: 0.5773 (t70)
REVERT: B  213 ASN cc_start: 0.7927 (t0) cc_final: 0.7639 (t0)
REVERT: C   40 MET cc_start: 0.4646 (pmm) cc_final: 0.4232 (pmm)
REVERT: D  116 MET cc_start: -0.0120 (tpp) cc_final: -0.0659 (tpp)
REVERT: D  199 MET cc_start: 0.2152 (tpp) cc_final: 0.1145 (mtp)
  outliers start: 36
  outliers final: 34
  residues processed: 228
  average time/residue: 0.1216
  time to fit residues: 42.5607
Evaluate side-chains
  230 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 195
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   24 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 THR
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks: [132, 66, 59, 180, 142, 19, 53, 74, 17, 157, 182]
   chunk 132 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 180 optimal weight:    6.9990
   chunk 142 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0270
   chunk 74 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 157 optimal weight:    9.9990
   chunk 182 optimal weight:    6.9990
   overall best weight:    1.8220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
** C  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 246 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.210708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.180965 restraints weight = 24758.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.181119 restraints weight = 27606.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.182764 restraints weight = 23739.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.183257 restraints weight = 17477.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.183695 restraints weight = 17164.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6146
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  17023  Z= 0.180
  Angle     :  0.926  50.980  23255  Z= 0.360
  Chirality :  0.046   0.364   2592
  Planarity :  0.004   0.056   2798
  Dihedral  : 16.713  64.176   2748
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.70 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.19), residues: 1926
  helix: -0.12 (0.21), residues: 599
  sheet: -0.74 (0.24), residues: 447
  loop : -1.67 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 847 
 TYR   0.023   0.002   TYR C 249 
 PHE   0.025   0.002   PHE A1109 
 TRP   0.015   0.002   TRP A1013 
 HIS   0.009   0.001   HIS A 342 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 (17019)
  covalent geometry    : angle       0.69615 /  0.36 (23243)
  hydrogen bonds       : bond        0.04028 /  2.61 (  755)
  hydrogen bonds       : angle       5.09069 /  3.62 ( 2093)
  metal coordination   : bond        0.01894 /  0.94 (    4)
  metal coordination   : angle      26.91733 / 17.49 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2340.34 seconds
wall clock time: 41 minutes 37.24 seconds (2497.24 seconds total)