Starting phenix.real_space_refine
on Tue Jul 29 12:24:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dgt_27429/07_2025/8dgt_27429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dgt_27429/07_2025/8dgt_27429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2025/8dgt_27429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2025/8dgt_27429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2025/8dgt_27429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dgt_27429/07_2025/8dgt_27429.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.066
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 9
    Type Number    sf(0)   Gaussians
     I       1     10.91       5
     Zn      2      6.06       5
     P      11      5.49       5
     Mg      2      5.21       5
     S      65      5.16       5
     C    6997      2.51       5
     N    1910      2.21       5
     O    2107      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11096
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3455
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 22, 'TRANS': 408}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2441
          Classifications: {'peptide': 311}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 293}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1846
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 5, 'TRANS': 223}
    Chain: "D"
      Number of atoms: 1833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1833
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 223}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "F"
      Number of atoms: 1398
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 167, 1324
          Classifications: {'peptide': 167}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 162}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 167, 1324
          Classifications: {'peptide': 167}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 162}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 1257
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' ZN': 2, 'AGS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "F"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GNP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    764  SG  CYS A 248      44.579  48.524  42.978  1.00 92.22           S
  ATOM    789  SG  CYS A 251      42.579  46.312  43.172  1.00 91.18           S
  ATOM    971  SG  CYS A 272      40.590  49.856  42.034  1.00 91.05           S
  ATOM    877  SG  CYS A 261      53.877  58.376  41.455  1.00 90.50           S
  ATOM    899  SG  CYS A 264      53.885  56.709  44.564  1.00 82.84           S
  ATOM   1029  SG  CYS A 280      54.516  60.397  43.977  1.00 77.32           S

  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   MET F   1 " occ=0.76
      ... (3 atoms not shown)
      pdb=" CB  MET F   1 " occ=0.76
    residue:
      pdb=" N   MET F  67 " occ=0.94
      ... (6 atoms not shown)
      pdb=" CE  MET F  67 " occ=0.94
    residue:
      pdb=" N   GLN F  70 " occ=0.97
      ... (7 atoms not shown)
      pdb=" NE2 GLN F  70 " occ=0.97
    residue:
      pdb=" N   TYR F  71 " occ=0.84
      ... (10 atoms not shown)
      pdb=" OH  TYR F  71 " occ=0.84
    residue:
      pdb=" N  AGLN F  99 " occ=0.58
      ... (16 atoms not shown)
      pdb=" NE2BGLN F  99 " occ=0.42
    residue:
      pdb=" N   GLU F 107 " occ=0.82
      ... (7 atoms not shown)
      pdb=" OE2 GLU F 107 " occ=0.82
    residue:
      pdb=" N   GLN F 150 " occ=0.97
      ... (7 atoms not shown)
      pdb=" NE2 GLN F 150 " occ=0.97
  Time building chain proxies: 8.19, per 1000 atoms: 0.74
  Number of scatterers: 11096
  At special positions: 0
  Unit cell: (98.88, 94.76, 127.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     I       1     52.95
     Zn      2     29.99
     S      65     16.00
     P      11     15.00
     Mg      2     11.99
     F       1      9.00
     O    2107      8.00
     N    1910      7.00
     C    6997      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.30
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 802 "
        pdb="ZN    ZN A 802 " - pdb=" ND1 HIS A 269 "
        pdb="ZN    ZN A 802 " - pdb=" SG  CYS A 272 "
        pdb="ZN    ZN A 802 " - pdb=" SG  CYS A 248 "
        pdb="ZN    ZN A 802 " - pdb=" SG  CYS A 251 "
      pdb="  ZN A 803 "
        pdb="ZN    ZN A 803 " - pdb=" SG  CYS A 280 "
        pdb="ZN    ZN A 803 " - pdb=" SG  CYS A 261 "
        pdb="ZN    ZN A 803 " - pdb=" ND1 HIS A 235 "
        pdb="ZN    ZN A 803 " - pdb=" SG  CYS A 264 "
      Number of angles added : 6


  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2612

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      57.0% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 176 through 187
      removed outlier: 4.895A  pdb=" N   LYS A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   ALA A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 195
    Processing helix  chain 'A' and resid 213 through 218
      removed outlier: 3.573A  pdb=" N   THR A 218 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 276
      removed outlier: 3.711A  pdb=" N   SER A 273 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   THR A 274 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 276 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 506
    Processing helix  chain 'A' and resid 536 through 543
    Processing helix  chain 'A' and resid 549 through 570
      removed outlier: 3.556A  pdb=" N   LYS A 570 " --> pdb=" O   TYR A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 580
      No H-bonds generated for 'chain 'A' and resid 578 through 580'
    Processing helix  chain 'A' and resid 586 through 588
      No H-bonds generated for 'chain 'A' and resid 586 through 588'
    Processing helix  chain 'A' and resid 621 through 627
    Processing helix  chain 'A' and resid 634 through 652
    Processing helix  chain 'A' and resid 661 through 671
      removed outlier: 3.899A  pdb=" N   ILE A 665 " --> pdb=" O   ASN A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 697
    Processing helix  chain 'A' and resid 700 through 704
    Processing helix  chain 'A' and resid 706 through 720
      removed outlier: 3.810A  pdb=" N   SER A 720 " --> pdb=" O   LEU A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 725
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.696A  pdb=" N   LYS B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 66
      No H-bonds generated for 'chain 'B' and resid 64 through 66'
    Processing helix  chain 'B' and resid 104 through 115
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 151 through 159
    Processing helix  chain 'B' and resid 162 through 183
      removed outlier: 3.645A  pdb=" N   LYS B 168 " --> pdb=" O   GLN B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 242 through 259
      removed outlier: 4.266A  pdb=" N   SER B 248 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 273
      removed outlier: 3.825A  pdb=" N   GLU B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 320
    Processing helix  chain 'B' and resid 331 through 342
    Processing helix  chain 'B' and resid 351 through 357
      removed outlier: 3.577A  pdb=" N   VAL B 357 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 367
    Processing helix  chain 'B' and resid 370 through 380
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 20 through 32
      removed outlier: 3.566A  pdb=" N   THR C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 70
      removed outlier: 3.596A  pdb=" N   ARG C  41 " --> pdb=" O   SER C  37 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN C  42 " --> pdb=" O   ASN C  38 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU C  43 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU C  44 " --> pdb=" O   GLU C  40 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL C  52 " --> pdb=" O   TYR C  48 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG C  55 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   GLU C  70 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 102
      removed outlier: 4.119A  pdb=" N   GLN C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 131
    Processing helix  chain 'C' and resid 137 through 160
      removed outlier: 3.507A  pdb=" N   ILE C 155 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 181
    Processing helix  chain 'C' and resid 184 through 202
      removed outlier: 3.863A  pdb=" N   GLU C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 210
      removed outlier: 3.607A  pdb=" N   SER C 210 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 207 through 210'
    Processing helix  chain 'C' and resid 211 through 229
    Processing helix  chain 'D' and resid 3 through 16
    Processing helix  chain 'D' and resid 19 through 33
      removed outlier: 3.543A  pdb=" N   VAL D  29 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR D  32 " --> pdb=" O   GLU D  28 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLY D  33 " --> pdb=" O   VAL D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 67
      removed outlier: 3.521A  pdb=" N   LEU D  44 " --> pdb=" O   GLU D  40 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL D  52 " --> pdb=" O   TYR D  48 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ARG D  55 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 89
      removed outlier: 3.594A  pdb=" N   ALA D  79 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLU D  81 " --> pdb=" O   GLN D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 104
      removed outlier: 3.549A  pdb=" N   CYS D  94 " --> pdb=" O   LEU D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 133
      removed outlier: 3.540A  pdb=" N   GLU D 131 " --> pdb=" O   ARG D 127 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   VAL D 132 " --> pdb=" O   TYR D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 160
      removed outlier: 3.930A  pdb=" N   ASN D 139 " --> pdb=" O   GLY D 135 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP D 144 " --> pdb=" O   SER D 140 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS D 147 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA D 152 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLU D 154 " --> pdb=" O   GLN D 150 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   ILE D 155 " --> pdb=" O   ASP D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 181
    Processing helix  chain 'D' and resid 184 through 202
    Processing helix  chain 'D' and resid 212 through 230
      removed outlier: 3.824A  pdb=" N   SER D 230 " --> pdb=" O   THR D 226 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 15 through 26
    Processing helix  chain 'F' and resid 61 through 63
      No H-bonds generated for 'chain 'F' and resid 61 through 63'
    Processing helix  chain 'F' and resid 64 through 75
      removed outlier: 3.626A  pdb=" N   THR F  74 " --> pdb=" O   GLN F  70 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 92
    Processing helix  chain 'F' and resid 92 through 105
    Processing helix  chain 'F' and resid 126 through 137
    Processing helix  chain 'F' and resid 151 through 167
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 208
      removed outlier: 4.484A  pdb=" N   VAL A 197 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   GLU F  37 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR F   2 " --> pdb=" O   LEU F  52 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ASP F  54 " --> pdb=" O   THR F   2 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   TYR F   4 " --> pdb=" O   ASP F  54 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   LEU F  56 " --> pdb=" O   TYR F   4 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   LEU F   6 " --> pdb=" O   LEU F  56 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   THR F  58 " --> pdb=" O   LEU F   6 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   VAL F   8 " --> pdb=" O   THR F  58 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   PHE F  78 " --> pdb=" O   VAL F 112 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   VAL F 114 " --> pdb=" O   PHE F  78 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   CYS F  80 " --> pdb=" O   VAL F 114 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ASN F 116 " --> pdb=" O   CYS F  80 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE F  82 " --> pdb=" O   ASN F 116 " (cutoff:3.500A)
      removed outlier: 8.770A  pdb=" N   ILE F 142 " --> pdb=" O   MET F 111 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU F 113 " --> pdb=" O   ILE F 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 241
    Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 465
      removed outlier: 7.440A  pdb=" N   GLY A 460 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS A 475 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ARG A 462 " --> pdb=" O   LYS A 473 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LYS A 473 " --> pdb=" O   ARG A 462 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 582 through 585
    Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 76
      removed outlier: 7.049A  pdb=" N   ILE B  71 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   SER B  86 " --> pdb=" O   ILE B  71 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   GLU B  73 " --> pdb=" O   LYS B  84 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LYS B  84 " --> pdb=" O   GLU B  73 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY B  75 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY B 131 " --> pdb=" O   CYS B 142 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLU B 144 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   PHE B 129 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150

    596 hydrogen bonds defined for protein.
    1726 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.20

  Time building geometry restraints manager: 3.77 seconds

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

  Histogram of bond lengths:
        1.18 -     1.37: 3707
        1.37 -     1.55: 7452
        1.55 -     1.74: 51
        1.74 -     1.92: 102
        1.92 -     2.11: 3
  Bond restraints: 11315
  Sorted by residual:
  bond pdb=" C   GLU A 225 "
       pdb=" N   VAL A 226 "
    ideal  model  delta    sigma   weight residual
    1.332  1.475 -0.143 1.36e-02 5.41e+03 1.10e+02
  bond pdb=" C18 LCJ B 403 "
       pdb=" N09 LCJ B 403 "
    ideal  model  delta    sigma   weight residual
    1.349  1.450 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" C11 LCJ B 403 "
       pdb=" N06 LCJ B 403 "
    ideal  model  delta    sigma   weight residual
    1.395  1.303  0.092 2.00e-02 2.50e+03 2.09e+01
  bond pdb=" N3B GNP F 202 "
       pdb=" PG  GNP F 202 "
    ideal  model  delta    sigma   weight residual
    1.801  1.711  0.090 2.00e-02 2.50e+03 2.03e+01
  bond pdb=" C10 LCJ B 403 "
       pdb=" N07 LCJ B 403 "
    ideal  model  delta    sigma   weight residual
    1.371  1.455 -0.084 2.00e-02 2.50e+03 1.75e+01
  ... (remaining 11310 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.67: 15298
        7.67 -    15.34: 7
       15.34 -    23.01: 0
       23.01 -    30.68: 1
       30.68 -    38.35: 2
  Bond angle restraints: 15308
  Sorted by residual:
  angle pdb=" O   GLU A 225 "
        pdb=" C   GLU A 225 "
        pdb=" N   VAL A 226 "
      ideal   model   delta    sigma   weight residual
     121.70   83.35   38.35 1.84e+00 2.95e-01 4.34e+02
  angle pdb=" C   MET F   1 "
        pdb=" N   THR F   2 "
        pdb=" CA  THR F   2 "
      ideal   model   delta    sigma   weight residual
     122.74   91.23   31.51 1.54e+00 4.22e-01 4.19e+02
  angle pdb=" CA  MET F   1 "
        pdb=" C   MET F   1 "
        pdb=" N   THR F   2 "
      ideal   model   delta    sigma   weight residual
     116.20   89.74   26.46 2.00e+00 2.50e-01 1.75e+02
  angle pdb=" CA  PRO A 152 "
        pdb=" N   PRO A 152 "
        pdb=" CD  PRO A 152 "
      ideal   model   delta    sigma   weight residual
     112.00   98.94   13.06 1.40e+00 5.10e-01 8.70e+01
  angle pdb=" CA  GLU A 225 "
        pdb=" C   GLU A 225 "
        pdb=" N   VAL A 226 "
      ideal   model   delta    sigma   weight residual
     116.18  125.88   -9.70 1.15e+00 7.56e-01 7.12e+01
  ... (remaining 15303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.56: 6617
       21.56 -    43.13: 260
       43.13 -    64.69: 84
       64.69 -    86.25: 10
       86.25 -   107.81: 4
  Dihedral angle restraints: 6975
    sinusoidal: 2927
      harmonic: 4048
  Sorted by residual:
  dihedral pdb=" O1B AGS B 402 "
           pdb=" O3B AGS B 402 "
           pdb=" PB  AGS B 402 "
           pdb=" PG  AGS B 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.91  176.72 -107.81     1      3.00e+01 1.11e-03 1.39e+01
  dihedral pdb=" CA  THR F  35 "
           pdb=" C   THR F  35 "
           pdb=" N   ILE F  36 "
           pdb=" CA  ILE F  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.82   18.18     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  THR F 144 "
           pdb=" C   THR F 144 "
           pdb=" N   SER F 145 "
           pdb=" CA  SER F 145 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 6972 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1501
       0.082 -    0.163: 160
       0.163 -    0.245: 29
       0.245 -    0.327: 3
       0.327 -    0.409: 2
  Chirality restraints: 1695
  Sorted by residual:
  chirality pdb=" CA  VAL A 157 "
            pdb=" N   VAL A 157 "
            pdb=" C   VAL A 157 "
            pdb=" CB  VAL A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.85   -0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" CA  VAL A 224 "
            pdb=" N   VAL A 224 "
            pdb=" C   VAL A 224 "
            pdb=" CB  VAL A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.77   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CB  ILE A 214 "
            pdb=" CA  ILE A 214 "
            pdb=" CG1 ILE A 214 "
            pdb=" CG2 ILE A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.95   -0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1692 not shown)

  Planarity restraints: 1954
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 225 "    0.133 2.00e-02 2.50e+03   2.00e-01 3.98e+02
        pdb=" C   GLU A 225 "   -0.345 2.00e-02 2.50e+03
        pdb=" O   GLU A 225 "    0.110 2.00e-02 2.50e+03
        pdb=" N   VAL A 226 "    0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET F   1 "    0.049 2.00e-02 2.50e+03   1.30e-01 1.68e+02
        pdb=" C   MET F   1 "   -0.223 2.00e-02 2.50e+03
        pdb=" O   MET F   1 "    0.100 2.00e-02 2.50e+03
        pdb=" N   THR F   2 "    0.074 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 151 "   -0.124 5.00e-02 4.00e+02   1.74e-01 4.85e+01
        pdb=" N   PRO A 152 "    0.301 5.00e-02 4.00e+02
        pdb=" CA  PRO A 152 "   -0.093 5.00e-02 4.00e+02
        pdb=" CD  PRO A 152 "   -0.083 5.00e-02 4.00e+02
  ... (remaining 1951 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.36: 32
        2.36 -     3.01: 6289
        3.01 -     3.66: 17197
        3.66 -     4.31: 26777
        4.31 -     4.96: 44600
  Nonbonded interactions: 94895
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 671 "
            pdb=" OD1BASP F  33 "
     model   vdw
     1.712 3.120
  nonbonded pdb=" OG  SER A 151 "
            pdb=" CD  PRO A 152 "
     model   vdw
     1.908 3.440
  nonbonded pdb="MG    MG F 201 "
            pdb=" O2G GNP F 202 "
     model   vdw
     2.027 2.170
  nonbonded pdb="MG    MG F 201 "
            pdb=" O2B GNP F 202 "
     model   vdw
     2.031 2.170
  nonbonded pdb=" OH  TYR A 673 "
            pdb=" OD1BASP F  33 "
     model   vdw
     2.062 3.040
  ... (remaining 94890 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ 
r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid  \ 
202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ 
h 230))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.16 max=1.00 mean=0.99
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:             3.400
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     32.600
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.050
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5263
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      :  0.007   0.209  11324  Z= 0.347
  Angle     :  0.936  38.349  15314  Z= 0.509
  Chirality :  0.055   0.409   1695
  Planarity :  0.008   0.200   1954
  Dihedral  : 13.248 107.814   4363
  Min Nonbonded Distance : 1.712

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.76 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  :  6.21 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.22), residues: 1359
  helix:  0.60 (0.19), residues: 710
  sheet: -0.53 (0.42), residues: 137
  loop : -1.18 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 216 
 HIS   0.008   0.001   HIS F  95 
 PHE   0.033   0.002   PHE A 160 
 TYR   0.023   0.002   TYR F  96 
 ARG   0.005   0.001   ARG F 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14121 (  596)
  hydrogen bonds       : angle       6.16729 ( 1726)
  metal coordination   : bond        0.13815 (    8)
  metal coordination   : angle      18.18594 (    6)
  covalent geometry    : bond        0.00587 (11315)
  covalent geometry    : angle       0.86449 (15308)
  Misc. bond           : bond        0.00673 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 461
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 PRO cc_start: 0.7225 (OUTLIER) cc_final: 0.6920 (Cg_exo)
REVERT: A  463 ILE cc_start: 0.8379 (mm) cc_final: 0.8008 (mm)
REVERT: A  475 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7709 (tptp)
REVERT: A  517 MET cc_start: 0.8055 (mmm) cc_final: 0.7784 (mtt)
REVERT: A  565 ASP cc_start: 0.7920 (t0) cc_final: 0.7663 (t70)
REVERT: A  580 ASN cc_start: 0.8153 (m110) cc_final: 0.7873 (m-40)
REVERT: A  721 LEU cc_start: 0.4799 (tp) cc_final: 0.4239 (tp)
REVERT: B  146 MET cc_start: 0.4725 (mmm) cc_final: 0.4254 (mmm)
REVERT: B  171 ILE cc_start: 0.8110 (mt) cc_final: 0.7830 (mt)
REVERT: B  188 HIS cc_start: 0.7378 (t-90) cc_final: 0.6969 (t-90)
REVERT: B  236 GLN cc_start: 0.7821 (mt0) cc_final: 0.7482 (tm-30)
REVERT: B  253 LEU cc_start: 0.8275 (mt) cc_final: 0.7364 (mt)
REVERT: B  329 VAL cc_start: 0.7523 (t) cc_final: 0.7226 (t)
REVERT: C   14 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8464 (tm-30)
REVERT: C   26 MET cc_start: 0.7632 (tpp) cc_final: 0.7349 (tpp)
REVERT: C   83 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7637 (tmm-80)
REVERT: C   96 ASP cc_start: 0.7774 (t70) cc_final: 0.6687 (t0)
REVERT: C   98 LEU cc_start: 0.8376 (mt) cc_final: 0.8089 (mm)
REVERT: C  118 TYR cc_start: 0.8431 (m-10) cc_final: 0.8172 (m-80)
REVERT: C  129 LEU cc_start: 0.9019 (mt) cc_final: 0.8383 (mp)
REVERT: C  146 GLN cc_start: 0.9118 (tp40) cc_final: 0.8914 (mm-40)
REVERT: C  167 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7265 (ttm170)
REVERT: C  177 PHE cc_start: 0.8573 (t80) cc_final: 0.8178 (t80)
REVERT: C  218 MET cc_start: 0.8164 (tpp) cc_final: 0.7542 (mmm)
REVERT: D   27 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7778 (ttpp)
REVERT: D   49 LYS cc_start: 0.7583 (tptm) cc_final: 0.7272 (ttmm)
REVERT: D  214 SER cc_start: 0.8010 (p) cc_final: 0.7451 (t)
REVERT: F   55 ILE cc_start: 0.3273 (mm) cc_final: 0.3050 (mt)
  outliers start: 32
  outliers final: 6
  residues processed: 485
  average time/residue: 0.3010
  time to fit residues: 193.7374
Evaluate side-chains
  266 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 259
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 PRO
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0370
   chunk 56 optimal weight:    6.9990
   chunk 34 optimal weight:    0.2980
   chunk 68 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0870
   chunk 121 optimal weight:    7.9990
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 562 GLN
A 585 HIS
A 628 GLN
A 661 ASN
B  56 GLN
B  87 HIS
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 GLN
B 339 ASN
D 207 ASN
F  27 HIS
F  70 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.227372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.196572 restraints weight = 53707.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.201689 restraints weight = 51592.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.207324 restraints weight = 14589.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4307 r_free = 0.4307    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4306 r_free = 0.4306    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.4306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11324  Z= 0.152
  Angle     :  0.666  10.042  15314  Z= 0.345
  Chirality :  0.043   0.226   1695
  Planarity :  0.005   0.076   1954
  Dihedral  :  8.165 105.829   1617
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.74 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1359
  helix:  1.23 (0.19), residues: 705
  sheet: -0.03 (0.43), residues: 135
  loop : -0.89 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.013   0.001   HIS A 725 
 PHE   0.025   0.002   PHE B 371 
 TYR   0.025   0.002   TYR B 229 
 ARG   0.007   0.001   ARG A 575 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  596)
  hydrogen bonds       : angle       4.85531 ( 1726)
  metal coordination   : bond        0.01176 (    8)
  metal coordination   : angle       2.46604 (    6)
  covalent geometry    : bond        0.00335 (11315)
  covalent geometry    : angle       0.66413 (15308)
  Misc. bond           : bond        0.00413 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 299
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 MET cc_start: 0.7653 (mmm) cc_final: 0.6789 (tpp)
REVERT: A  565 ASP cc_start: 0.7901 (t0) cc_final: 0.7644 (t70)
REVERT: A  575 ARG cc_start: 0.8557 (ttm170) cc_final: 0.8321 (ttm110)
REVERT: A  699 LYS cc_start: 0.8147 (mttp) cc_final: 0.7678 (tttm)
REVERT: A  730 GLU cc_start: 0.8265 (tp30) cc_final: 0.8064 (tp30)
REVERT: B  170 SER cc_start: 0.8221 (m) cc_final: 0.7993 (p)
REVERT: B  260 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6774 (ttp80)
REVERT: C   26 MET cc_start: 0.7531 (tpp) cc_final: 0.7066 (tpp)
REVERT: C  118 TYR cc_start: 0.8429 (m-10) cc_final: 0.8192 (m-80)
REVERT: D   49 LYS cc_start: 0.7937 (tptm) cc_final: 0.7631 (ttmm)
REVERT: D   98 LEU cc_start: 0.8420 (mt) cc_final: 0.8206 (mt)
REVERT: D  222 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7804 (ttp-110)
REVERT: F   55 ILE cc_start: 0.3431 (mm) cc_final: 0.3110 (mm)
REVERT: F   72 MET cc_start: 0.6159 (ttm) cc_final: 0.5829 (ttm)
REVERT: F   78 PHE cc_start: 0.3966 (m-80) cc_final: 0.3521 (m-80)
  outliers start: 38
  outliers final: 23
  residues processed: 322
  average time/residue: 0.2740
  time to fit residues: 123.2225
Evaluate side-chains
  264 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain F residue  150 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0370
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 585 HIS
B 243 GLN
C  67 GLN
C 146 GLN
** F  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.220906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.185509 restraints weight = 55251.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.187499 restraints weight = 34610.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.181843 restraints weight = 18437.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3982
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3982 r_free = 0.3982    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3982 r_free = 0.3982    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  11324  Z= 0.182
  Angle     :  0.682  12.002  15314  Z= 0.349
  Chirality :  0.044   0.222   1695
  Planarity :  0.005   0.074   1954
  Dihedral  :  8.191 106.374   1614
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 18.48 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.23), residues: 1359
  helix:  1.19 (0.19), residues: 711
  sheet:  0.14 (0.43), residues: 142
  loop : -0.83 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 476 
 HIS   0.009   0.001   HIS A 585 
 PHE   0.016   0.002   PHE B  53 
 TYR   0.019   0.002   TYR D 118 
 ARG   0.008   0.001   ARG A 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  596)
  hydrogen bonds       : angle       4.69638 ( 1726)
  metal coordination   : bond        0.02476 (    8)
  metal coordination   : angle       2.90606 (    6)
  covalent geometry    : bond        0.00424 (11315)
  covalent geometry    : angle       0.67936 (15308)
  Misc. bond           : bond        0.00991 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 252
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  260 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6848 (ttp80)
REVERT: C   92 GLU cc_start: 0.7049 (tp30) cc_final: 0.6780 (tp30)
REVERT: C  118 TYR cc_start: 0.8313 (m-10) cc_final: 0.7947 (m-80)
REVERT: D   88 LYS cc_start: 0.8116 (tppt) cc_final: 0.7709 (tptp)
REVERT: F   55 ILE cc_start: 0.3824 (mm) cc_final: 0.3435 (mm)
REVERT: F  150 GLN cc_start: 0.0784 (OUTLIER) cc_final: 0.0396 (pt0)
  outliers start: 46
  outliers final: 29
  residues processed: 279
  average time/residue: 0.2353
  time to fit residues: 92.7879
Evaluate side-chains
  250 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 219
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain F residue  150 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 132 optimal weight:   40.0000
   chunk 29 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
C  67 GLN
C 146 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.218681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.183038 restraints weight = 55690.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.183192 restraints weight = 33793.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.179454 restraints weight = 17048.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  11324  Z= 0.174
  Angle     :  0.644  10.405  15314  Z= 0.328
  Chirality :  0.044   0.217   1695
  Planarity :  0.005   0.090   1954
  Dihedral  :  8.090 109.077   1614
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.55 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.23), residues: 1359
  helix:  1.06 (0.19), residues: 730
  sheet:  0.11 (0.43), residues: 145
  loop : -0.84 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 476 
 HIS   0.013   0.001   HIS A 725 
 PHE   0.022   0.002   PHE A 160 
 TYR   0.020   0.002   TYR D 118 
 ARG   0.009   0.001   ARG A 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  596)
  hydrogen bonds       : angle       4.59272 ( 1726)
  metal coordination   : bond        0.02720 (    8)
  metal coordination   : angle       2.59539 (    6)
  covalent geometry    : bond        0.00405 (11315)
  covalent geometry    : angle       0.64182 (15308)
  Misc. bond           : bond        0.00387 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 248
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 TRP cc_start: 0.7875 (t60) cc_final: 0.7388 (t60)
REVERT: A  564 MET cc_start: 0.7361 (mmm) cc_final: 0.6635 (tpp)
REVERT: A  650 MET cc_start: 0.8256 (tpp) cc_final: 0.7668 (mmt)
REVERT: B  219 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7228 (tmm)
REVERT: B  260 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6934 (ttp80)
REVERT: C   92 GLU cc_start: 0.7212 (tp30) cc_final: 0.6978 (tp30)
REVERT: C  118 TYR cc_start: 0.8319 (m-10) cc_final: 0.7896 (m-80)
REVERT: D   88 LYS cc_start: 0.8110 (tppt) cc_final: 0.7709 (tptp)
REVERT: F   27 HIS cc_start: 0.7305 (t-90) cc_final: 0.7048 (p90)
REVERT: F   55 ILE cc_start: 0.3916 (mm) cc_final: 0.3472 (mm)
REVERT: F  150 GLN cc_start: 0.1050 (OUTLIER) cc_final: 0.0713 (pt0)
  outliers start: 49
  outliers final: 30
  residues processed: 270
  average time/residue: 0.2266
  time to fit residues: 87.3353
Evaluate side-chains
  257 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 224
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  153 PHE
Chi-restraints excluded: chain F residue  150 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 121 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0670
   chunk 113 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 44 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    1.1324

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 GLN
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 GLN
C 146 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.215711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.183386 restraints weight = 52554.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.188084 restraints weight = 49360.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.193439 restraints weight = 15740.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4116 r_free = 0.4116    target_work(ls_wunit_k1) = 0.184         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4114 r_free = 0.4114    target_work(ls_wunit_k1) = 0.184         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.4114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.5360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  11324  Z= 0.169
  Angle     :  0.638   7.948  15314  Z= 0.330
  Chirality :  0.043   0.208   1695
  Planarity :  0.005   0.074   1954
  Dihedral  :  8.058 108.646   1614
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 19.39 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1359
  helix:  1.14 (0.19), residues: 727
  sheet:  0.14 (0.43), residues: 145
  loop : -0.89 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 476 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.021   0.002   PHE A 250 
 TYR   0.034   0.002   TYR C  48 
 ARG   0.019   0.001   ARG A 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  596)
  hydrogen bonds       : angle       4.57696 ( 1726)
  metal coordination   : bond        0.02706 (    8)
  metal coordination   : angle       2.91184 (    6)
  covalent geometry    : bond        0.00394 (11315)
  covalent geometry    : angle       0.63529 (15308)
  Misc. bond           : bond        0.00376 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 246
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 TRP cc_start: 0.7708 (t60) cc_final: 0.7392 (t60)
REVERT: A  564 MET cc_start: 0.7406 (mmm) cc_final: 0.6559 (tpp)
REVERT: A  571 SER cc_start: 0.8524 (m) cc_final: 0.8233 (t)
REVERT: A  650 MET cc_start: 0.8000 (tpp) cc_final: 0.7458 (mmt)
REVERT: B  103 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8339 (tp)
REVERT: B  219 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7327 (tmm)
REVERT: B  260 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6862 (ttp80)
REVERT: C  118 TYR cc_start: 0.8490 (m-10) cc_final: 0.8136 (m-80)
REVERT: D   87 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7417 (tp30)
REVERT: D   88 LYS cc_start: 0.8207 (tppt) cc_final: 0.7717 (tptp)
REVERT: D  121 MET cc_start: 0.7554 (ttm) cc_final: 0.7334 (ttm)
REVERT: D  160 MET cc_start: 0.6326 (ptp) cc_final: 0.5872 (ptp)
REVERT: F   27 HIS cc_start: 0.7578 (t-90) cc_final: 0.7125 (p90)
REVERT: F   55 ILE cc_start: 0.3838 (mm) cc_final: 0.3388 (mm)
  outliers start: 52
  outliers final: 32
  residues processed: 278
  average time/residue: 0.2088
  time to fit residues: 84.4757
Evaluate side-chains
  249 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 214
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   46 GLN
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue  153 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 120 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 282 ASN
A 568 HIS
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 GLN
C  67 GLN
** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  50 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.209086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.176725 restraints weight = 57486.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.181780 restraints weight = 48177.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.186339 restraints weight = 14203.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4021 r_free = 0.4021    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4021 r_free = 0.4021    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.5991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090  11324  Z= 0.268
  Angle     :  0.753   9.579  15314  Z= 0.387
  Chirality :  0.047   0.219   1695
  Planarity :  0.005   0.065   1954
  Dihedral  :  8.477 109.633   1612
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 21.62 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.23), residues: 1359
  helix:  0.82 (0.18), residues: 725
  sheet:  0.13 (0.45), residues: 130
  loop : -0.89 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 476 
 HIS   0.009   0.001   HIS A 269 
 PHE   0.020   0.002   PHE B 371 
 TYR   0.020   0.002   TYR C 125 
 ARG   0.022   0.001   ARG F  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  596)
  hydrogen bonds       : angle       4.89811 ( 1726)
  metal coordination   : bond        0.03662 (    8)
  metal coordination   : angle       5.86121 (    6)
  covalent geometry    : bond        0.00620 (11315)
  covalent geometry    : angle       0.74427 (15308)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 234
  time to evaluate  : 1.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.7216 (ttm) cc_final: 0.6694 (tpp)
REVERT: A  650 MET cc_start: 0.7892 (tpp) cc_final: 0.7485 (mmt)
REVERT: A  664 GLN cc_start: 0.7801 (tp40) cc_final: 0.7581 (tp40)
REVERT: A  734 ASN cc_start: 0.7890 (t0) cc_final: 0.7486 (t0)
REVERT: B  111 ILE cc_start: 0.9569 (mt) cc_final: 0.9353 (mm)
REVERT: B  122 ASN cc_start: 0.7257 (m-40) cc_final: 0.5833 (p0)
REVERT: B  187 MET cc_start: 0.6706 (pmm) cc_final: 0.6300 (ptm)
REVERT: B  219 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7328 (tmm)
REVERT: B  260 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7019 (ttp80)
REVERT: D   50 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8689 (t0)
REVERT: D   78 MET cc_start: 0.6031 (tpp) cc_final: 0.5673 (tpp)
REVERT: D   88 LYS cc_start: 0.8333 (tppt) cc_final: 0.7952 (tptp)
REVERT: D   98 LEU cc_start: 0.8369 (mt) cc_final: 0.7980 (mt)
REVERT: D  121 MET cc_start: 0.7755 (ttm) cc_final: 0.7466 (ttm)
REVERT: F   27 HIS cc_start: 0.7558 (t-90) cc_final: 0.7087 (p-80)
REVERT: F   55 ILE cc_start: 0.4114 (mm) cc_final: 0.3519 (mt)
  outliers start: 50
  outliers final: 33
  residues processed: 264
  average time/residue: 0.2611
  time to fit residues: 100.7580
Evaluate side-chains
  241 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 205
  time to evaluate  : 1.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   50 ASN
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue  116 VAL
Chi-restraints excluded: chain D residue  153 PHE
Chi-restraints excluded: chain F residue   97 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 127 optimal weight:    0.9980
   chunk 126 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 568 HIS
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 GLN
C  67 GLN
C 146 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.213244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.181404 restraints weight = 48633.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.186454 restraints weight = 45519.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.191293 restraints weight = 14384.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4120 r_free = 0.4120    target_work(ls_wunit_k1) = 0.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4120 r_free = 0.4120    target_work(ls_wunit_k1) = 0.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
moved from start:          0.6208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.322  11324  Z= 0.166
  Angle     :  0.699  16.040  15314  Z= 0.353
  Chirality :  0.044   0.209   1695
  Planarity :  0.005   0.070   1954
  Dihedral  :  8.263 110.435   1608
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 23.78 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.23), residues: 1359
  helix:  1.00 (0.19), residues: 728
  sheet:  0.06 (0.44), residues: 145
  loop : -0.92 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 476 
 HIS   0.034   0.002   HIS A 269 
 PHE   0.020   0.002   PHE A 250 
 TYR   0.017   0.002   TYR C 125 
 ARG   0.018   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  596)
  hydrogen bonds       : angle       4.68107 ( 1726)
  metal coordination   : bond        0.11753 (    8)
  metal coordination   : angle       8.51561 (    6)
  covalent geometry    : bond        0.00363 (11315)
  covalent geometry    : angle       0.67887 (15308)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 231
  time to evaluate  : 1.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.7270 (ttm) cc_final: 0.6731 (tpp)
REVERT: A  564 MET cc_start: 0.7335 (mmm) cc_final: 0.6504 (tpp)
REVERT: A  571 SER cc_start: 0.8623 (m) cc_final: 0.8334 (t)
REVERT: A  650 MET cc_start: 0.7800 (tpp) cc_final: 0.7325 (mmt)
REVERT: A  664 GLN cc_start: 0.7686 (tp40) cc_final: 0.7419 (tp40)
REVERT: B  111 ILE cc_start: 0.9483 (mt) cc_final: 0.9199 (mm)
REVERT: B  187 MET cc_start: 0.6547 (pmm) cc_final: 0.6141 (ptm)
REVERT: B  219 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7383 (tmm)
REVERT: B  260 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6970 (ttp80)
REVERT: C  174 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8344 (t80)
REVERT: C  178 TYR cc_start: 0.7707 (m-10) cc_final: 0.7485 (m-10)
REVERT: D   78 MET cc_start: 0.5865 (tpp) cc_final: 0.5647 (tpp)
REVERT: D   87 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7344 (tp30)
REVERT: D   88 LYS cc_start: 0.8285 (tppt) cc_final: 0.7840 (tptp)
REVERT: D   92 GLU cc_start: 0.6838 (pm20) cc_final: 0.6219 (pm20)
REVERT: D  121 MET cc_start: 0.7460 (ttm) cc_final: 0.7215 (ttm)
REVERT: D  150 GLN cc_start: 0.7836 (tp40) cc_final: 0.7509 (tp40)
REVERT: F   27 HIS cc_start: 0.7318 (t-90) cc_final: 0.7097 (p-80)
REVERT: F   55 ILE cc_start: 0.3994 (mm) cc_final: 0.3597 (mm)
REVERT: F  159 LEU cc_start: 0.6340 (tp) cc_final: 0.5856 (tp)
  outliers start: 39
  outliers final: 27
  residues processed: 256
  average time/residue: 0.2380
  time to fit residues: 88.9695
Evaluate side-chains
  248 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 218
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue  100 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  174 PHE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  153 PHE
Chi-restraints excluded: chain F residue   97 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 118 optimal weight:   30.0000
   chunk 107 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 GLN
C  67 GLN
C 146 GLN
F  61 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.211747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.176448 restraints weight = 59308.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.177618 restraints weight = 30939.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.171378 restraints weight = 16637.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3913 r_free = 0.3913    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.6493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.259  11324  Z= 0.184
  Angle     :  0.714  12.106  15314  Z= 0.361
  Chirality :  0.046   0.267   1695
  Planarity :  0.005   0.058   1954
  Dihedral  :  8.450 108.075   1608
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.69 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.23), residues: 1359
  helix:  0.92 (0.18), residues: 728
  sheet:  0.08 (0.44), residues: 144
  loop : -0.87 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 476 
 HIS   0.027   0.001   HIS A 269 
 PHE   0.020   0.002   PHE F  28 
 TYR   0.017   0.002   TYR C 125 
 ARG   0.015   0.001   ARG F  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  596)
  hydrogen bonds       : angle       4.75199 ( 1726)
  metal coordination   : bond        0.09775 (    8)
  metal coordination   : angle       6.86769 (    6)
  covalent geometry    : bond        0.00415 (11315)
  covalent geometry    : angle       0.70133 (15308)
  Misc. bond           : bond        0.00503 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 227
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.7301 (ttm) cc_final: 0.6776 (tpp)
REVERT: A  519 TYR cc_start: 0.7941 (p90) cc_final: 0.7736 (p90)
REVERT: A  564 MET cc_start: 0.7249 (mmm) cc_final: 0.6433 (tpp)
REVERT: B  111 ILE cc_start: 0.9412 (mt) cc_final: 0.9136 (mm)
REVERT: B  143 MET cc_start: 0.6155 (mtp) cc_final: 0.5603 (mtp)
REVERT: B  187 MET cc_start: 0.6526 (pmm) cc_final: 0.6280 (ptm)
REVERT: B  219 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7428 (tmm)
REVERT: B  260 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7086 (ttp80)
REVERT: D   78 MET cc_start: 0.5805 (tpp) cc_final: 0.5597 (tpp)
REVERT: D   88 LYS cc_start: 0.8264 (tppt) cc_final: 0.7825 (tptp)
REVERT: D   92 GLU cc_start: 0.6857 (pm20) cc_final: 0.6369 (pm20)
REVERT: D  118 TYR cc_start: 0.7803 (m-80) cc_final: 0.7529 (m-80)
REVERT: D  121 MET cc_start: 0.7353 (ttm) cc_final: 0.7101 (ttm)
REVERT: F   55 ILE cc_start: 0.4220 (mm) cc_final: 0.3609 (mt)
REVERT: F  159 LEU cc_start: 0.5838 (tp) cc_final: 0.5446 (tp)
  outliers start: 40
  outliers final: 32
  residues processed: 254
  average time/residue: 0.3502
  time to fit residues: 131.0386
Evaluate side-chains
  244 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 1.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  100 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   87 GLU
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain F residue   61 GLN
Chi-restraints excluded: chain F residue   97 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 111 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 GLN
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.210963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.176633 restraints weight = 58808.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.175394 restraints weight = 31080.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.171956 restraints weight = 17375.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3895 r_free = 0.3895    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3895 r_free = 0.3895    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.6554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.265  11324  Z= 0.318
  Angle     :  0.953  59.199  15314  Z= 0.534
  Chirality :  0.049   0.691   1695
  Planarity :  0.007   0.211   1954
  Dihedral  :  8.449 107.973   1608
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 25.35 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.23), residues: 1359
  helix:  0.91 (0.18), residues: 728
  sheet:  0.05 (0.44), residues: 144
  loop : -0.89 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 476 
 HIS   0.030   0.002   HIS A 542 
 PHE   0.048   0.002   PHE A 160 
 TYR   0.070   0.002   TYR B 130 
 ARG   0.075   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  596)
  hydrogen bonds       : angle       4.74738 ( 1726)
  metal coordination   : bond        0.09203 (    8)
  metal coordination   : angle       6.81429 (    6)
  covalent geometry    : bond        0.00655 (11315)
  covalent geometry    : angle       0.94329 (15308)
  Misc. bond           : bond        0.00406 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 3.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.7376 (ttm) cc_final: 0.6829 (tpp)
REVERT: A  564 MET cc_start: 0.7167 (mmm) cc_final: 0.6351 (tpp)
REVERT: B  111 ILE cc_start: 0.9387 (mt) cc_final: 0.9105 (mm)
REVERT: B  175 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8252 (mtmm)
REVERT: B  187 MET cc_start: 0.6535 (pmm) cc_final: 0.6232 (ptm)
REVERT: B  219 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7429 (tmm)
REVERT: B  260 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7075 (ttp80)
REVERT: D   88 LYS cc_start: 0.8261 (tppt) cc_final: 0.7824 (tptp)
REVERT: D  121 MET cc_start: 0.7267 (ttm) cc_final: 0.7028 (ttm)
REVERT: F   55 ILE cc_start: 0.4121 (mm) cc_final: 0.3536 (mt)
REVERT: F  159 LEU cc_start: 0.5811 (tp) cc_final: 0.5384 (tp)
  outliers start: 39
  outliers final: 35
  residues processed: 238
  average time/residue: 0.4060
  time to fit residues: 145.6422
Evaluate side-chains
  243 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  100 HIS
Chi-restraints excluded: chain B residue  175 LYS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   87 GLU
Chi-restraints excluded: chain D residue  116 VAL
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain F residue    6 LEU
Chi-restraints excluded: chain F residue   97 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 109 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 146 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 = 0.4379 r_free = 0.4379 target = 0.210976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.174184 restraints weight = 58146.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.177506 restraints weight = 32832.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.173147 restraints weight = 15943.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3915 r_free = 0.3915    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.6569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.265  11324  Z= 0.318
  Angle     :  0.953  59.199  15314  Z= 0.534
  Chirality :  0.049   0.691   1695
  Planarity :  0.007   0.211   1954
  Dihedral  :  8.449 107.973   1608
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 19.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 25.60 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.23), residues: 1359
  helix:  0.91 (0.18), residues: 728
  sheet:  0.05 (0.44), residues: 144
  loop : -0.89 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 476 
 HIS   0.030   0.002   HIS A 542 
 PHE   0.048   0.002   PHE A 160 
 TYR   0.070   0.002   TYR B 130 
 ARG   0.075   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  596)
  hydrogen bonds       : angle       4.74738 ( 1726)
  metal coordination   : bond        0.09203 (    8)
  metal coordination   : angle       6.81429 (    6)
  covalent geometry    : bond        0.00655 (11315)
  covalent geometry    : angle       0.94329 (15308)
  Misc. bond           : bond        0.00406 (    1)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 2.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.7365 (ttm) cc_final: 0.6823 (tpp)
REVERT: A  564 MET cc_start: 0.7220 (mmm) cc_final: 0.6413 (tpp)
REVERT: B  111 ILE cc_start: 0.9391 (mt) cc_final: 0.9111 (mm)
REVERT: B  175 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8258 (mtmm)
REVERT: B  187 MET cc_start: 0.6507 (pmm) cc_final: 0.6238 (ptm)
REVERT: B  219 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7422 (tmm)
REVERT: B  260 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7078 (ttp80)
REVERT: D   88 LYS cc_start: 0.8304 (tppt) cc_final: 0.7838 (tptp)
REVERT: D  121 MET cc_start: 0.7311 (ttm) cc_final: 0.7073 (ttm)
REVERT: F   55 ILE cc_start: 0.4105 (mm) cc_final: 0.3518 (mt)
REVERT: F  159 LEU cc_start: 0.5796 (tp) cc_final: 0.5370 (tp)
  outliers start: 38
  outliers final: 35
  residues processed: 228
  average time/residue: 0.3905
  time to fit residues: 131.0939
Evaluate side-chains
  243 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 1.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  585 HIS
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  100 HIS
Chi-restraints excluded: chain B residue  175 LYS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  239 HIS
Chi-restraints excluded: chain B residue  260 ARG
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   87 GLU
Chi-restraints excluded: chain D residue  116 VAL
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain F residue    6 LEU
Chi-restraints excluded: chain F residue   97 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0980
   chunk 1 optimal weight:    7.9990
   chunk 125 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 112 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 146 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 = 0.4379 r_free = 0.4379 target = 0.210975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.179232 restraints weight = 52500.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.184674 restraints weight = 47220.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.189530 restraints weight = 13528.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4052 r_free = 0.4052    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4052 r_free = 0.4052    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.4052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.6569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.265  11324  Z= 0.318
  Angle     :  0.953  59.199  15314  Z= 0.534
  Chirality :  0.049   0.691   1695
  Planarity :  0.007   0.211   1954
  Dihedral  :  8.449 107.973   1608
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 19.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 25.68 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.23), residues: 1359
  helix:  0.91 (0.18), residues: 728
  sheet:  0.05 (0.44), residues: 144
  loop : -0.89 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 476 
 HIS   0.030   0.002   HIS A 542 
 PHE   0.048   0.002   PHE A 160 
 TYR   0.070   0.002   TYR B 130 
 ARG   0.075   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  596)
  hydrogen bonds       : angle       4.74738 ( 1726)
  metal coordination   : bond        0.09203 (    8)
  metal coordination   : angle       6.81429 (    6)
  covalent geometry    : bond        0.00655 (11315)
  covalent geometry    : angle       0.94329 (15308)
  Misc. bond           : bond        0.00406 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4655.41 seconds
wall clock time: 86 minutes 49.41 seconds (5209.41 seconds total)